Tagged microorganisms and methods of tagging

ABSTRACT

The present invention provides methods for tagging and/or identifying microorganisms. In some preferred embodiments, the microorganisms are bacteria. In some particularly preferred embodiments, the bacteria are members of the genus  Streptococcus , while in other embodiments, the bacteria are members of other genera. The present invention also provides microorganisms tagged using the methods set forth herein. In some preferred embodiments, the tagged microorganisms are bacteria. In some particularly preferred embodiments, the tagged bacteria are members of the genus  Streptococcus , while in other embodiments, the tagged bacteria are members of other genera.

The present application claims priority to U.S. Prov. Pat. Appln. Ser.No. 60/747,682, filed May 19, 2006, and U.S. Prov. Pat. Appln. Ser. No.60/904,721, filed Mar. 2, 2007.

FIELD OF THE INVENTION

The present invention provides methods for tagging and/or identifyingmicroorganisms. In some preferred embodiments, the microorganisms arebacteria. In some particularly preferred embodiments, the bacteria aremembers of the genus Streptococcus, while in other embodiments, thebacteria are members of other genera. The present invention alsoprovides microorganisms tagged using the methods set forth herein. Insome preferred embodiments, the tagged microorganisms are bacteria. Insome particularly preferred embodiments, the tagged bacteria are membersof the genus Streptococcus, while in other embodiments, the taggedbacteria are members of other genera.

BACKGROUND OF THE INVENTION

Microbial strains, especially those used as starter cultures for thefermented food/beverage industry are highly selected and characterizedfor specific functionalities. Typically, these starter cultures arecommercially sold as live organisms and often remain viable in the endproduct. Thus, it is possible to isolate, identify and characterize thestarter culture strains by culturing the microorganisms present in theend products. In addition, it is then possible to utilize these starterculture strains in other products, including competitive products. It isdifficult to monitor the use of such strains by others, includingcompetitors. Indeed, there is a need in the art for methods to easilytag cultures in order to identity their source(s) and monitor their usein various products.

SUMMARY OF THE INVENTION

The present invention provides methods for tagging and/or identifyingmicroorganisms. In some preferred embodiments, the microorganisms arebacteria. In some particularly preferred embodiments, the bacteria aremembers of the genus Streptococcus, while in other embodiments, thebacteria are members of other genera. The present invention alsoprovides microorganisms tagged using the methods set forth herein. Insome preferred embodiments, the tagged microorganisms are bacteria. Insome particularly preferred embodiments, the tagged bacteria are membersof the genus Streptococcus, while in other embodiments, the taggedbacteria are members of other genera.

In some embodiments, the present invention provides methods forlabelling or tagging a bacterium comprising the steps of: (a) exposing aparent bacterium to a bacteriophage; (b) selecting a bacteriophageinsensitive mutant; (c) comparing a CRISPR locus or a portion thereoffrom the parent bacterium and the bacteriophage insensitive mutant; and(d) selecting a tagged bacterium comprising an additional repeat-spacerunit in the CRISPR locus that is not present in the parent bacterium. Insome preferred embodiments, the tagged bacterium is obtained orobtainable by the method according to the present invention. In furtherembodiments, the present invention provides cell cultures comprising thetagged bacterium.

The present invention also provides food product and/or feed productscomprising the tagged bacterium and/or cell cultures comprising at leastone tagged bacterial species. In yet additional embodiments, the presentinvention provides processes for preparing food and/or feed productscomprising the tagged bacteria and/or cell cultures comprising at leastone tagged bacterial species. In some embodiments, the present inventionprovides methods for preparing food and/or feed comprising the step ofadding the tagged bacterium or the cell culture to said food product orfeed. In yet additional embodiments, the present invention provides foodand/or feed obtained or obtainable using the methods of the presentinvention.

In additional embodiments, the present invention provides methods forgenerating CRISPR variants, comprising the steps of: (a) exposing aparent bacterium to a bacteriophage; (b) selecting a bacteriophageresistant bacterium; (c) comparing the CRISPR locus or a portion thereoffrom the parent bacterium and the bacteriophage insensitive mutant; (d)selecting a tagged bacterium comprising an additional repeat-spacer unitin the CRISPR locus that is not present in the parent bacterium; and (e)isolating and/or cloning and/or sequencing the additional repeat-spacerunit. The present invention also provides CRISPR variants obtained orobtainable using the methods of the present invention.

In some additional embodiments, the present invention also providescompositions and methods for the use of at least one nucleotide sequenceobtained or obtainable from a bacteriophage for tagging and/oridentifying a bacterium, wherein the phage nucleotide sequence isintegrated within the CRISPR locus of the parent bacterium. In somealternative embodiments, the present invention provides methods andcompositions for using a nucleotide sequence for labelling and/oridentifying a bacterium, wherein the nucleotide sequence is obtained orobtainable by: (a) exposing a parent bacterium to a bacteriophage; (b)selecting a bacteriophage insensitive mutant; (c) comparing a CRISPRlocus or a portion thereof from the parent bacterium and thebacteriophage insensitive mutant; and (d) selecting a tagged bacteriumcomprising an additional repeat-spacer unit in the CRISPR locus that isnot present in the parent bacterium. In additional embodiments, thepresent invention also provides methods for identifying tagged bacteria,comprising the step of screening the bacteria for an additionalrepeat-spacer unit within a CRISPR locus of the bacterium.

In some further embodiments, the present invention provides methods foridentifying a tagged bacterium comprising the steps of: (a) screeningthe bacterium for an additional repeat-spacer unit in a CRISPR locus;(b) determining the nucleotide sequence of the additional repeat-spacerunit; (c) comparing the nucleotide sequence of the additionalrepeat-spacer unit with a database of tagged bacteria obtained orobtainable by the method of the present invention; and (d) identifying anucleotide sequence in the database of tagged bacteria that matches theadditional repeat-spacer unit.

In some embodiments, the 5′ end and/or the 3′ end of the CRISPR locus ofthe parent bacterium is/are compared. In some particularly preferredembodiments, at least the first CRISPR repeat and/or the first CRISPRspacer (e.g., the first CRISPR spacer core) at the 5′ end of the CRISPRlocus is/are compared. In still further embodiments, at least the lastCRISPR repeat and/or the last CRISPR spacer (e.g., the last CRISPRspacer core) at the 3′ end of the CRISPR locus is/are compared. Inadditional preferred embodiments of the methods of the presentinvention, the methods comprise the step of selecting a tagged bacteriumcomprising an additional repeat-spacer unit at the 5′ end and/or at the3′ end of the CRISPR locus that is not present in the parent bacterium.In some embodiments, the methods of the present invention compriseexposing the parent bacterium to two or more bacteriophage eithersimultaneously or sequentially.

In some further embodiments, the CRISPR locus or at least a portionthereof from the parent bacterium and the bacteriophage insensitivemutant are compared by amplifying the CRISPR locus or a portion thereoffrom the parent bacterium and/or the bacteriophage insensitive mutant.In some preferred embodiments, amplification is accomplished using PCR.In some additional embodiments, the CRISPR locus or at least a portionthereof from the parent bacterium and the bacteriophage insensitivemutant are compared by sequencing the CRISPR locus or a portion thereoffrom the parent bacterium and/or the bacteriophage insensitive mutant.In some particularly preferred embodiments, the CRISPR locus or at leasta portion thereof from the parent bacterium and the bacteriophageinsensitive mutant are compared by amplifying and then sequencing theCRISPR locus or a portion thereof from the parent bacterium and/or thebacteriophage insensitive mutant. In some embodiments, the additionalrepeat-spacer unit is at least 44 nucleotides in length. In some furtherembodiments, a tagged bacterium comprising two or three or moreadditional repeat-spacer units is selected. In some preferredembodiments, the additional repeat-spacer unit comprises at least onenucleotide sequence that has at least about 95% identity, or morepreferably, about 100% identity to a CRISPR repeat in the CRISPR locusof the parent bacterium. In some alternative preferred embodiments, theadditional repeat-spacer unit comprises at least one nucleotide sequencethat has at least 95% identity, preferably, 100% identity to anucleotide sequence in the genome of the bacteriophage used for theselection of the tagged bacterium.

In some alternative preferred embodiments, the additional repeat-spacerunit comprises a first nucleotide sequence that has at least about 95%identity, or more preferably, about 100% identity to a CRISPR repeat inthe CRISPR locus of the parent bacterium and a second nucleotidesequence that has at least one nucleotide sequence that has at leastabout 95% identity, or more preferably, about 100% identity to anucleotide sequence in the genome of the bacteriophage used for theselection of the tagged bacterium.

In some alternative preferred embodiments, the methods provided by thepresent invention for identifying a tagged bacterium comprise theadditional step of comparing the additional repeat-spacer unit with abacteriophage sequence database and/or a bacterial sequence database.

In some preferred embodiments, the parent bacterium is suitable for useas a starter culture, a probiotic culture and/or a dietary supplement.In some preferred embodiments, the parent bacterium is selected from thegroup of genera consisting of: Escherichia, Shigella, Salmonella,Erwinia, Yersinia, Bacillus, Vibrio, Legionella, Pseudomonas, Neisseria,Bordetella, Helicobacter, Listeria, Agrobacterium, Staphylococcus,Streptococcus, Enterococcus, Clostridium, Corynebacterium,Mycobacterium, Treponema, Borrelia, Francisella, Brucella,Bifidobacterium, Brevibacterium, Propionibacterium, Laciococcus,Lactobacillus, Pediococcus, Leuconostoc and Oenococcus. In someembodiments, the present invention finds use with cell cultures,including but not limited to starter cultures, probiotic cultures and/ordietary supplements.

In some further preferred embodiments, the bacteriophage is selectedfrom the group of virus families consisting of: Corticoviridae,Cystoviridae, Inoviridae, Leviviridae, Microviridae, Myoviridae,Podoviridae, Siphoviridae, and Tectiviridae.

In some embodiments, the present invention provides S. thermophiluscomprising a sequence obtained or obtainable from a bacteriophage,wherein said sequence comprises SEQ ID NO:3 and/or 4. In someembodiments, the present invention provides S. thermophilus comprising asequence obtained or obtainable from a bacteriophage, wherein thesequence comprises SEQ ID NO:3 and/or 4 located downstream (e.g.,directly downstream) of the first CRISPR repeat in at least one CRISPRlocus. In yet further embodiments, the present invention provides S.thermophilus comprising a sequence obtained or obtainable from abacteriophage, wherein the sequence comprises SEQ ID NO:9. In somepreferred embodiments, the S. thermophilus comprises a sequence obtainedor obtainable from a bacteriophage, wherein the sequence comprises SEQID NO:9 downstream (e.g., directly downstream) of the first CRISPRrepeat in at least one CRISPR locus. In yet further embodiments, thepresent invention provides S. thermophilus comprising a sequenceobtained or obtainable from a bacteriophage, wherein the sequencecomprises SEQ ID NO:11. In still further embodiments, the S.thermophilus comprises a sequence obtained or obtainable from abacteriophage, wherein said sequence comprises SEQ ID NO:11 downstream(e.g., directly downstream) of the first CRISPR repeat in at least oneCRISPR locus.

The present invention provides methods for tagging a bacteriumcomprising the steps of: exposing at least one parent bacteriumcomprising at least a portion of a CRISPR locus to at least oneexogenous nucleic acid sequence to produce at least one tagged bacteriumcomprising a modified CRISPR locus, wherein the modified CRISPR locuscomprises at least one additional repeat-spacer unit than the CRISPRlocus of the parent bacterium and wherein the additional repeat-spacerunit comprises a tag; and comparing at least a portion of the CRISPRlocus of the parent bacterium and the modified CRISPR locus of saidtagged bacterium. In some embodiments, the exogenous nucleic acidsequence is selected from bacteriophages, plasmids, megaplasmids,transposable elements, transposons, and insertion sequences. In someparticularly preferred embodiments, the exogenous nucleic acid comprisesat least a portion of the genome of at least one bacteriophage. In somealternative particularly preferred embodiments, the tagged bacterium isa bacteriophage insensitive mutant. In some additional embodiments, the5′ end and/or the 3′ end of the CRISPR locus of the parent bacterium iscompared with the modified CRISPR locus of the tagged bacterium. Inadditional embodiments, the 5′ and/or the 3′ end of at least the firstCRISPR repeat and/or at least the first CRISPR spacer of the CRISPRlocus of the parent bacterium is compared with the modified CRISPR locusof the tagged bacterium. In some further embodiments, the methodsfurther comprise the step of selecting at least one tagged bacterium. Inyet additional embodiments, the parent bacterium is simultaneously orsequentially exposed to two or more bacteriophages. In some preferredembodiments, the tagged bacterium comprises at least one additionalrepeat-spacer unit. In some alternative embodiments, at least a portionof the CRISPR locus of the parent bacterium and at least a portion ofthe modified CRISPR locus of the tagged bacterium are compared byamplifying at least a portion of the CRISPR locus and at least a portionof the modified CRISPR locus, to produce an amplified CRISPR locussequence and an amplified modified CRISPR locus sequence. In somepreferred embodiments, amplifying comprises the use of the polymerasechain reaction. In some alternative preferred embodiments, at least aportion of the CRISPR locus of the parent bacterium and at least aportion of the modified CRISPR locus of said the bacterium are comparedby sequencing at least a portion of the CRISPR locus and at least aportion of the modified CRISPR locus. In some additional embodiments,the methods further comprise the step of sequencing the amplified CRISPRlocus sequence and the amplified modified CRISPR sequence locus. In somepreferred embodiments, the additional repeat-spacer unit comprises atleast about 44 nucleotides. In some additional embodiments, theadditional repeat-spacer unit comprises at least one nucleotide sequencethat has at least 95% identity to a CRISPR repeat in the CRISPR locus ofthe parent bacterium. In some further embodiments, the additionalrepeat-spacer unit comprises at least one nucleotide sequence that hasat least 95% identity to a nucleotide sequence in the genome of at leastone bacteriophage. In yet additional embodiments, the tagged bacteriumfurther comprises at least one additional nucleotide sequence that hasat least 95% identity to a nucleotide sequence in the genome of at leastone bacteriophage. In some preferred embodiments, the parent bacteriumis an industrially useful culture. In some particularly preferredembodiments, the parent bacterium comprises a culture selected fromstarter cultures, probiotic cultures, and dietary supplement cultures.In some further particularly preferred embodiments, the parent bacteriumis selected from Escherichia, Shigella, Salmonella, Erwinia, Yersinia,Bacillus, Vibrio, Legionella, Pseudomonas, Neisseria, Bordetella,Helicobacter, Listeria, Agrobacterium, Staphylococcus, Streptococcus,Enterococcus, Clostridium, Corynebacterium, Mycobacterium, Treponema,Borrelia, Francisella, Brucella, Bifidobacterium, Brevibacterium,Propionibacterium, Lactococcus, Lactobacillus, Pediococcus, Leuconostocand Oenococcus. In some further embodiments, the at least onebacteriophage is selected from the group of virus families consistingof: Corticoviridae, Cystoviridae, Inoviridae, Leviviridae, Microviridae,Myoviridae, Podoviridae, Siphoviridae, and Tectiviridae.

The present invention also provides tagged bacteria obtained using themethods set forth herein. In some preferred embodiments, the taggedbacterium is an industrially useful culture. In some alternativeembodiments, the present invention provides cell cultures comprising thetagged bacteria produced using the methods set forth herein. In someadditional embodiments, the cell culture comprising tagged bacteriacomprises an industrially useful culture. In some particularly preferredembodiments, the tagged bacterium comprises a culture selected fromstarter cultures, probiotic cultures and dietary supplement cultures. Inyet additional embodiments, the present invention provides food and/orfeed comprising tagged bacterium obtained using the methods set forthherein.

The present invention also provides methods for preparing food and/orfeed comprising the use of tagged bacteria, wherein tagged bacteria areadded to the food or feed. In some additional embodiments, the cellculture comprising tagged bacteria comprises an industrially usefulculture. In some particularly preferred embodiments, the taggedbacterium comprises a culture selected from starter cultures, probioticcultures and dietary supplement cultures. In yet additional embodiments,the present invention provides food and/or feed comprising taggedbacterium obtained using the methods set forth herein.

The present invention also provides methods for generating at least oneCRISPR variant comprising a tag, comprising the steps of: exposing aparent bacterium comprising at least a portion of a CRISPR locus to atleast one bacteriophage to produce a culture of bacteriophage resistantvariant bacteria comprising a modified CRISPR locus; selectingbacteriophage resistant variant bacteria; comparing the CRISPR locus ora portion thereof of the parent bacterium and the modified CRISPR locusof the bacteriophage insensitive variant, to identify bacteriophageinsensitive variants comprising at least one tag, wherein at least onetag comprises at least one additional nucleic acid fragment in themodified CRISPR locus that is absent from the CRISPR locus of the parentbacterium; selecting the bacteriophage insensitive variants comprising atag; and analyzing at least one tag. In some preferred embodiments, theanalysis is accomplished using any suitable method known in the art. Insome particularly preferred embodiments, the analysis is selected fromisolating, cloning and sequencing. The present invention also providesat least one CRISPR variant obtained using the methods set forth herein.In some additional embodiments, the present invention provides cellcultures comprising at least one CRISPR variant produced using themethods provided herein. In yet additional embodiments, the presentinvention provides food and/or feed comprising at least one CRISPRvariant produced using the methods set forth herein. In some additionalembodiments, at least one tag is integrated into the CRISPR locus of theparent bacterium to produce at least one CRISPR variant.

The present invention also provides methods for identifying a taggedbacterium comprising at least one CRISPR locus, comprising the steps of:screening a tagged bacterium the presence of a tag in the CRISPR locus;determining the nucleotide sequence of the tag; comparing the nucleotidesequence of the tag with nucleotide sequences present in at least onedatabase; and identifying a nucleotide sequence in the database thatshares homology with the tag. In some embodiments, the databasecomprises nucleotide sequences of tagged bacteria. In some furtherembodiments, the database is selected from bacteriophage sequencedatabases and bacterial sequence databases.

DESCRIPTION OF THE FIGURES

FIG. 1 illustrates one embodiment of the present invention in which atagging sequence and a CRISPR repeat are integrated at one end of theCRISPR locus. Panel A shows a CRISPR locus and element including repeats(R), spacers (S), the upstream leader and downstream trailer, with theterminal repeat (RD adjacent to the trailer, and cas genes in thevicinity (4 cas genes named cas1 to cas4 in this example, not drawn toscale). cas genes can be on either end, or split and present on bothends. Cas genes may be located on any of the two DNA strands. Panel Bshows a phage sequence in black, with a fragment of the sequence (Sn)being used as an additional spacer (i.e., tagging sequence). Panel Cshows the insertion of a new spacer (Sn) (i.e., tagging sequence) at oneend of the CRISPR locus (close to the leader in this example at the 5′end of the CRISPR locus), between two repeats. Panel D provides acomparison of the CRISPR locus content between the parent and the mutantbacterium (i.e., tagged bacterium), with a new spacer (Sn) (i.e.,tagging sequence) integrated at one end of the CRISPR locus (close tothe leader in this example), between repeats. The new spacer (Sn)constitutes the tagging sequence which is specific for the mutantbacterium (i.e., tagged bacterium). In some embodiments, this processresults in the addition of one or more spacers from the phage sequence.

FIG. 2 illustrates one embodiment of the present invention in which twotagging sequences and two CRISPR repeats are integrated at one end ofthe CRISPR locus. Panel A shows a CRISPR locus and elements, includingrepeats (R), spacers (S), the upstream leader and downstream trailer,with the terminal repeat (RT) adjacent to the trailer, and cas genes inthe vicinity (4 cas genes named cas1 to cas4 in this example, not drawnto scale). Cas genes can be on either end, or split and present on bothends. Cas genes may be located on any of the two DNA strands. Panel Bshows a phage sequence in black, with two fragments of the sequence (Snand Sn′) being used as additional spacers (i.e., tagging sequences).Panel C illustrates insertion of the new spacers (i.e., taggingsequences) (Sn and Sn′) at the same end of the CRISPR locus (close tothe leader in this example at the 5′ end), each in-between two repeats.Panel D provides a comparison of the CRISPR locus content between theparent and the mutant bacterium (i.e., tagged bacterium), with two newspacers (Sn and Sn′) integrated at the same end of the CRISPR locus(close to the leader in this example at the 5′ end), each in betweenrepeats. The new spacers Sn and Sn′ constitute the tagging sequencewhich is specific of the mutant. In some embodiments, this processresults in the addition of one or more spacers from the phage sequence.

FIG. 3 provides a schematic representation of the CRISPR1 locus of S.thermophilus DGCC7710 and tagged variants. The CRISPR1 locus ofDGCC7710(WT) is at the top. In this Figure, arrowed boxes representgenes in the vicinity of CRISPR1. The spacer-repeat region of WT is inthe middle, with repeats (black diamonds), spacers (numbered grayboxes), leader (L, white box), and terminal repeat (T, black diamond)indicated. At the bottom, tagged variants are represented with 1, 2 or 4added repeat-spacer units (black diamonds associated with S+n whitebox). The combination of the added repeat-spacer units represents thetag. In this Figure, the new numbering system of the cas genes is used.Previously, the cas genes were numbered cas 1, cas2, cas3, and cas4.Now, the cas genes are numbered cas5, cas1, cas6, and cas7. Thus, tocorrelate the designations in FIGS. 1 and 2, with those in FIGS. 3 and4, cas1 in FIGS. 1 and 2 is referred to as cas5 in FIGS. 3 and 4; cas2in FIGS. 1 and 2 is cas1 in FIGS. 3 and 4; cas3 in FIGS. 1 and 2 is cas6in FIGS. 3 and 4; and cas4 in FIGS. 1 and 2 is cas7 in FIGS. 3 and 4.

FIG. 4 provides a schematic representation of the CRISPR1 locus of S.thermophilus DCGG7710 and positioning of detection-PCR primers. The samesymbols are used as in FIG. 3. The positions of the forward primer andreverse primer are indicated. Also, as indicated in the description ofFIG. 3 above, the new numbering system of the cas genes is used.Previously, the cas genes were numbered cas1, cas2, cas3, and cas4. Now,the cas genes are numbered cas5, cas1, cas6, and cas7. Thus, tocorrelate the designations in FIGS. 1 and 2, with those in FIGS. 3 and4, cas1 in FIGS. 1 and 2 is referred to as cas5 in FIGS. 3 and 4; cas2in FIGS. 1 and 2 is cas1 in FIGS. 3 and 4; cas3 in FIGS. 1 and 2 is cas6in FIGS. 3 and 4; and cas4 in FIGS. 1 and 2 is cas7 in FIGS. 3 and 4.

FIG. 5 provides a sequence comparison of part of the sequence of theCRISPR1 locus of the isolate obtained from the fermented milk productwith the sequence of the CRISPR1 locus of DGCC7710 (SEQ ID NO:1), withthe CRISPR1 consensus repeat sequence (SEQ ID NO:74) and with thesequence of the additional spacer sequence in DGCC_(phi2972) ^(S41) (SEQID NO:75). The leader sequence of CRISPR1 is shown in lowercase, therepeat sequences are boxed, and the other sequences correspond to spacersequences.

DESCRIPTION OF THE INVENTION

The present invention provides methods for tagging and/or identifyingmicroorganisms. In some preferred embodiments, the microorganisms arebacteria. In some particularly preferred embodiments, the bacteria aremembers of the genus Streptococcus, while in other embodiments, thebacteria are members of other genera. The present invention alsoprovides microorganisms tagged using the methods set forth herein. Insome preferred embodiments, the tagged microorganisms are bacteria. Insome particularly preferred embodiments, the tagged bacteria are membersof the genus Streptococcus, while in other embodiments, the taggedbacteria are members of other genera.

There is a need for methods and compositions useful in theidentification of specific bacterial strains, in order to determinetheir origin. Although it is feasible to insert a syntheticoligonucleotide into a strain to tag or label it using recombinant DNAtechnologies, the tagged strain would be considered to be a geneticallymodified organism and would be likely to face regulatory issues incommercial applications.

In addition, the preparation of cultures is labor intensive, occupyingmuch space and equipment, and there is a considerable risk ofcontamination with spoilage bacteria and/or phages during thepropagation steps. The failure of bacterial cultures due tobacteriophage (phage) infection and multiplication is a major problemwith the industrial use of bacterial cultures. There are many differenttypes of phages and new strains continue to emerge. Thus, there is aneed for methods and compositions for tracking and monitoring bacteriaused in such cultures.

When a bacterial population is infected with a virulent bacteriophagemany of the cells are killed by the bacteriophage. However, spontaneousphage-resistant mutants are often produced. Thesebacteriophage-resistant bacteria correspond to a subpopulation ofbacteria that are able to withstand and survive bacteriophage infection.These resistant bacteria are referred to herein as “bacteriophageresistant mutants,” “bacteriophage insensitive mutants,” “BIMs,” “taggedbacteria,” “tagged bacterium,” “labelled bacteria,” or “labelledbacterium.”

As described herein, when a bacteriophage infects a bacterium, one ormore sequences originating from the bacteriophage genome are integratedinto (e.g., within) the CRISPR locus of the bacterium, while in otherembodiments, integration occurs in other locations within thebacterium's genome. Indeed, in some embodiments, “bacteriophageresistant mutants”/“bacteriophage insensitive mutants”/“BIMs” havebacteriophage sequence integrated in CRISPR while in other embodiments,strains have other type of chromosomal mutation. However, it is intendedthat tagged bacteria are produced due to integration of phage sequenceintegration into CRISPR. Thus, the bacteriophage-derivable or derivedsequence is new to the CRISPR locus of the bacterium and provides a“label” or “tag,” which is identifiable by its location and/or sequenceand/or adjacent sequence. It has also been found that a duplicatedsequence (e.g., a duplicated CRISPR repeat) originating from the parentbacterium is also integrated iteratively, sequentially, simultaneouslyor substantially simultaneously along with the sequence originating fromthe bacteriophage genome.

In addition, in some embodiments, independent infection of a culture(e.g., a pure culture) of a given bacterial strain using the samevirulent bacteriophage leads to the integration of one or more differentbacteriophage sequences into the CRISPR locus of the bacterial strain.In some preferred embodiments, the integration of differentbacteriophage sequences in the CRISPR locus of the bacterial strain is arandom event. However, in some other embodiments, the integration is nota random occurrence. Once it is integrated it is maintained and thusbecomes a robust means to tag and/or track a bacterium. Thus, the one ormore sequences originating from the bacteriophage genome are not onlynew to the CRISPR locus of the parent bacterium but are also a tag thatis unique to each bacterium. Thus, the present invention providescompositions and methods for tagging (i.e., labelling) and/oridentifying a bacterium. Furthermore, the methods and compositions ofthe present invention are particularly advantageous because the methodis a ‘natural’ method that does not result in a genetically modifiedorganism. Accordingly, labelled or tagged bacteria prepared according tothe methods of the present invention are not considered to begenetically modified, since the bacteria have been created by a naturalbiological process of bacteriophage infection.

The present invention provides methods for the use of a sequenceobtained or obtainable from a bacteriophage (e.g., in the manufacture ofa tagged bacterium) for tagging and/or identifying a bacterium, whereinthe sequence is integrated at one end of the CRISPR locus of a parentbacterium. In some preferred embodiments, the present invention providesmethods for the use of a sequence obtained or obtainable from abacteriophage (e.g., in the manufacture of a tagged bacterium) fortagging and/or identifying a bacterium, wherein the sequence comprises:(i) at least one sequence that is homologous (e.g., identical) to aCRISPR repeat in the CRISPR locus of the bacterium; and (ii) a taggingsequence. In further embodiments, the present invention provides methodsfor the use of a sequence for tagging and/or identifying a bacterium(e.g., in the manufacture of a tagged bacterium), wherein the sequenceis obtained or obtainable by: (a) exposing a parent bacterium to abacteriophage; (b) selecting a bacteriophage insensitive mutant; (c)comparing the CRISPR locus or a portion thereof from the parentbacterium and the bacteriophage insensitive mutant; and (d) selecting asequence in the CRISPR locus or a portion thereof of the bacteriophageinsensitive mutant that is not present in the parent bacterium.

In some additional embodiments, the present invention provides nucleicacid sequences (e.g., recombinant or an isolated nucleic acid sequence)consisting essentially of at least one gene or protein. In someembodiments, the nucleic acid sequence is DNA, while in otherembodiments, it is RNA. Nucleic acid from any suitable origin finds usein the present invention, including genomic, synthetic or recombinantnucleic acid (e.g., cDNA). However, in some particularly preferredembodiments, the sequence is a naturally-occurring nucleic acidsequence. In some embodiments, the nucleotide sequence isdouble-stranded, while in other embodiments, it is single-stranded. Insome further embodiments, the nucleic acid sequence represents the sensestrand, while in other embodiments it represents the antisense strand orcombinations thereof. Recombinant nucleic acid sequences prepared usingany suitable recombinant technique known the art find use in the presentinvention. In some preferred embodiments the target nucleic acidsequence is or is derived from a gene. In some particularly preferredembodiments, the nucleic acid sequence is an “exogenous nucleic acidsequence” which is introduced into a parent bacterium using any suitablemethod known in the art, including but not limited to natural andrecombinant methods. In some most particularly preferred embodiments,the exogenous nucleic acid sequence comprises at least a portion of abacteriophage genome. In some additional particularly preferredembodiments, the exogenous nucleic acid sequence is introduced into aparent bacterium through exposure of the bacterium to at least onebacteriophage.

In some embodiments, the nucleic acid sequence and the nucleic acidsencompassed by the present invention are isolated or substantiallypurified. As used herein, the terms “isolated” or “substantiallypurified” refer to nucleic acid molecules, biologically activefragments, variants, homologues, or derivatives thereof that aresubstantially or essentially free from components normally found inassociation with the nucleic acid in its natural state. Such componentsinclude other cellular material, culture media from recombinantproduction, and various chemicals used in chemically synthesising thenucleic acids. In some embodiments, an “isolated” nucleic acid sequenceor nucleic acid is typically free of nucleic acid sequences that flankthe nucleic acid of interest in the genomic DNA of the organism fromwhich the nucleic acid was derived (e.g., coding sequences present atthe 5′ or 3′ ends). However, in some embodiments, the molecule includessome additional bases or moieties that do not deleteriously affect thebasic characteristics of the composition.

The nucleic acid sequence(s) find use engineering cells (e.g., arecipient cell). In some embodiments, the nucleic acid sequence isinserted into the DNA (e.g., plasmid DNA or genomic DNA) of a recipientcell using any suitable method known in the art (e.g., homologousrecombination). In other embodiments, nucleic acid sequence(s) find useas templates upon which to modify (e.g., mutate) the DNA of a cell(e.g., a recipient cell) such as plasmid DNA or genomic DNA, underconditions such that the nucleic acid sequence(s) are created in the DNAof the cell. In some preferred embodiments, the nucleic acid sequence(s)are cloned (e.g., into a construct, plasmid or a vector) which is thenused to transform the cell using any suitable method known in the art.

The present invention provides methods and compositions utilizingvariants, homologues, derivatives and fragments thereof. The term“variant” is used herein in reference to a naturally occurringpolypeptide or nucleotide sequences which differs from a wild-typesequence. As used herein, the term “fragment,” refers to a polypeptideor nucleotide sequence that comprises a fraction of a wild-typesequence. In some embodiments, fragments comprise one or more largecontiguous sections of sequence or a plurality of small sections. Insome embodiments, the sequence also comprises other elements. Forexample, in some embodiments, it is a fusion protein that includesanother protein sequence. In some preferred embodiments, the sequencecomprises at least about 50%, more preferably at least about 65%, morepreferably at least about 80%, more preferably at least about 85%, morepreferably at least 90%, more preferably at least 95%, more preferablyat least 96%, more preferably at least about 97%, more preferably atleast about 98%, or most preferably at least about 99% of the wild-typesequence.

In some particularly preferred embodiments, the fragment is a functionalfragment. As used herein, a “functional fragment” of a molecule refersto a fragment retaining or possessing substantially the same biologicalactivity as the intact molecule. In particularly preferred embodiments,functional fragments retain at least about 10%. In other embodiments, atleast about 25%, about 50%, about 75%, about 80%, about 85%, about 90%,about 95%, about 96%, about 97%, about 98%, or about 99% of thebiological activity of the intact molecule. In alternative embodiments,the fragment retains about 50%, more preferably about 60%, morepreferably about 70%, more preferably about 80%, more preferably about85%, more preferably about 90%, more preferably about 95%, morepreferably about 96%, more preferably about 97%, more preferably about98%, or most preferably about 99% activity of the wild-type polypeptideor nucleotide sequence.

As used herein, the term “homologue” refers to an entity having acertain homology with the subject amino acid sequences and the subjectnucleotide sequences. As used particularly herein, the term “homology”is synonymous with “identity.” In the present context, a homologoussequence is taken to include an amino acid sequence, which is at leastabout 75, about 85 or about 90% identical, preferably at least about95%, about 96%, about 97%, about 98% or about 99% identical to thesubject sequence. Although homology can also be considered in terms ofsimilarity (i.e., amino acid residues having similar chemicalproperties/functions), in the context of the present invention it ispreferred to express homology in terms of sequence identity. In somepreferred embodiments, a homologous sequence comprises a nucleotidesequence, which is at least about 75, about 85 or about 90% identical,preferably at least about 95%, about 96%, about 97%, about 98%, or about99% identical to the subject sequence (i.e., the sequence of interestused as a reference). In some embodiments, homology comparisons areconducted by eye, although other methods known in the art find use(e.g., with the aid of readily available sequence comparison programs).Commercially available computer programs are capable of calculating thepercent homology (% homology) between two or more sequences, and thusfind use in the present invention. Indeed methods and systems arereadily commercially available for such analyses. Additionaldescriptions of some suitable methods, as well as methods andcompositions suitable for substitutions, etc., are provided in U.S.Prov. Appin. Ser. No. 60/904,701, filed Mar. 2, 2007.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods for tagging and/or identifyingmicroorganisms. In some preferred embodiments, the microorganisms arebacteria. In some particularly preferred embodiments, the bacteria aremembers of the genus Streptococcus, while in other embodiments, thebacteria are members of other genera. The present invention alsoprovides microorganisms tagged using the methods set forth herein. Insome preferred embodiments, the tagged microorganisms are bacteria. Insome particularly preferred embodiments, the tagged bacteria are membersof the genus Streptococcus, while in other embodiments, the taggedbacteria are members of other genera.

A. CRISPRs and CRISPR Loci

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats);also known as SPIDRs—SPacer Interspersed Direct Repeats) constitute afamily of recently described DNA loci that are usually specific to aparticular bacterial species. The CRISPR locus is a distinct class ofinterspersed short sequence repeats (SSRs) that were first recognized inE. coli (Ishino et al., J. Bacteriol., 169:5429-5433 [1987]; and Nakataet al., J. Bacteriol. 171:3553-3556 [1989]). Similar interspersed SSRshave been identified in Haloferax medilerranei, Streptococcus pyogenes,Anabaena, and Mycobacterium tuberculosis (See, Groenen et al., Mol.Microbiol. 10:1057-1065 [1993]; Hoe et al., Emerg. Infect. Dis.,5:254-263 [1999]; Masepohl et al., Biochim. Biophys. Acta 1307:26-30[1996]; and Mojica et al., Mol. Microbiol. 17:85-93 [1995]). The CRISPRloci differ from other SSRs by the structure of the repeats, which havebeen termed short regularly spaced repeats (SRSRs) (Janssen et al.,OMICS J. Integ. Biol., 6:23-33 [2002]; and Mojica et al., Mol.Microbiol. 36:244-246 [2000]). The repeats are short elements that occurin clusters that are always regularly spaced by unique interveningsequences with a constant length (Mojica et al., [2000], supra).Although the repeat sequences are highly conserved between strains, thenumber of interspersed repeats and the sequences of the spacer regionsdiffer from strain to strain (van Embden et al., J. Bacteriol.,182:2393-2401 [2000]).

CRISPR loci consist of short and highly conserved partially palindromicDNA repeats typically of 24 to 40 bp. These repeats have been reportedto occur in a range from 1 to 249. Although isolated elements have beendetected, they are generally arranged in clusters (up to about 20 ormore per genome) of repeated units spaced by unique intervening 20-58 bysequences. To date, up to 20 distinct CRISPR loci have been found withina single chromosome. CRISPRs are generally homogenous within a givengenome with most of them being identical. However, there are examples ofheterogeneity in, for example, the Archaea (Mojica et al., [2000],supra).

As used herein, the term “CRISPR locus” refers to the DNA segment whichincludes all of the CRISPR repeats, starting with the first nucleotideof the first CRISPR repeat and ending with the last nucleotide of thelast (terminal) CRISPR repeat. In some alternative embodiments, “atleast a portion” of at least one CRISPR locus finds use. Thus, it isintended that the present invention encompass embodiments in which atleast one entire CRISPR locus is used, as well as embodiments in whichat least a portion (i.e., part of at least one CRISPR locus).

Although the biological function of CRISPR loci is unknown, somehypotheses have been proposed. For example, it has been proposed thatthey may be involved in the attachment of the chromosome to a cellularstructure, or in the chromosome replication and replicon partitioning(Jansen et al., OMICS 6:23-33 [2002]; Jansen et al., Mol. Microbiol.,43:1565-1575 [2002]; and Pourcel et al., Microbiol., 151:653-663[2005]). Mojica et al. (Mojica et al., J. Mol. Evol., 60:174-182 [2005])hypothesize that CRISPR may be involved in conferring specific immunityagainst foreign DNA and Pourcel et al. (supra) hypothesize that CRISPRsare structures that are able to take up pieces of foreign DNA as part ofa defense mechanism. Bolotin et al. (supra) suggest that the CRISPRspacer elements are the traces of past invasions by extrachromosomalelements, and hypothesize that they provide a cell with immunity againstphage infection, and more generally foreign DNA expression, by coding ananti-sense RNA. Bolotin et al. (supra) also suggest that car genes arenecessary for CRISPR formation. However, it is not intended that thepresent invention be limited to any particular mechanism, function,theory, nor means of action.

B. Identifying CRISPR Loci

Various methods for identifying CRISPR loci are known in the art. Forexample, Jensen et al. (Jensen et al., [2002], supra) describe acomputer-based approach in which nucleotide sequences are searched forCRISPR motifs using the PATSCAN program at the server of the Mathematicsand Computer Science Division at the Argonne National Laboratory,Argonne, Ill., USA. The algorithm that was used for identifying CRISPRmotifs was p1=a . . . bc . . . d p1c . . . d p1c . . . dp1, where a andb were the lower and upper size limit of the repeat and p1 and c and dwere the lower and upper size limit of the spacer sequences. The valuesof a, b, c and d may be varied from about 15 to about 70 bp atincrements of about 5 bp. In some preferred embodiments, CRISPR loci areidentified using dotplots (e.g., by using the Dotter computer program).

Any suitable method known in the art finds use in analyzing sequencesimilarity. For example, analysis may be performed using NCB1 BLAST witha microbial genomes database and GenBank, as known in the art. Inaddition, nucleotide sequences, including those provided herein areincluded in databases (e.g., GenBank or the JG1 genome website).

In additional embodiments, the methods of the present invention utilizeamplification procedures (See e.g., Mojica et al., [2005], supra; andPourcel et al., [2005], supra). Amplification of the desired region ofDNA may be achieved by any method known in the art, including polymerasechain reaction (PCR). “Amplification” refers to the production ofadditional copies of a nucleic acid sequence. This is generally carriedout using PCR technologies. The “polymerase chain reaction” (“PCR”) iswell-known to those in the art. In the present invention,oligonucleotide primers are designed for use in PCR. reactions toamplify all or part of a CRISPR locus. The term “primer” refers to anoligonucleotide, whether occurring naturally as in a purifiedrestriction digest or produced synthetically, which is capable of actingas a point of initiation of synthesis when placed under conditions inwhich synthesis of a primer extension product which is complementary toa nucleic acid strand is induced (i.e., in the presence of nucleotidesand an inducing agent, such as DNA polymerase and at a suitabletemperature and pH). In some embodiments, the primer is single strandedfor maximum efficiency in amplification, although in other embodiments,the primer is double stranded. In some embodiments, the primer is anoligodeoxyribonucleotide. The primer must be sufficiently long to primethe synthesis of extension products in the presence of the inducingagent. The exact length of the primers depends on many factors includingtemperature, source of primer, and the use of the method. PCR primersare typically at least about 10 nucleotides in length, and mosttypically at least about 20 nucleotides in length. Methods for designingand conducting PCR are well known in the art, and include, but are notlimited to methods using paired primers, nested primers, single specificprimers, degenerate primers, gene-specific primers, vector-specificprimers, partially mismatched primers, etc.

In some preferred embodiments of the present invention, a CRISPR locusor a portion thereof from a parent bacterium and a tagged bacterium arecompared using any suitable method known in the art. In some preferredembodiments of the present invention, the CRISPR locus or a portionthereof from the parent bacterium and the tagged bacterium are comparedby amplifying the CRISPR locus or a portion thereof. In addition towell-known cycling amplification methods (e.g., PCR, ligase chainreaction, etc.), other methods, including but not limited to isothermalamplification methods find use in the present invention. Well-knownisothermal amplification methods that find use in the present inventioninclude, but are not limited to strand displacement amplification (SDA),Q-beta-replicase, nucleic acid-based sequence amplification (NASBA), andself-sustained sequence replication.

In some other preferred embodiments of the present invention, the CRISPRlocus or a portion thereof from the parent bacterium and the taggedbacterium are compared by sequencing the CRISPR locus or a portionthereof from the parent bacterium and the tagged bacterium. In somealternative embodiments, they are compared by amplifying and thensequencing the CRISPR loci or a portion thereof. In some embodiments,one end of the CRISPR loci from parent and tagged bacteria are compared,while in other embodiments, both the 5′ and 3′ ends of the loci arecompared. In some preferred embodiments, one end (e.g., the 5′ end) ofthe CRISPR loci are compared. In yet other embodiments, at least thelast CRISPR repeat at the 3′ end of the CRISPR locus and/or at least thelast CRISPR spacer (e.g., the last CRISPR spacer core) at the 3′ end ofthe CRISPR locus and/or at least the first CRISPR repeat at the 5′ endof the CRISPR locus and/or at least the first CRISPR spacer (e.g., thefirst CRISPR spacer core) at the 5′ end of the CRISPR locus arecompared. In some preferred embodiments, at least the first CRISPRrepeat at the 5′ end of the CRISPR locus and/or at least the firstCRISPR spacer (e.g., the first CRISPR spacer core) at the 5′ end of theCRISPR locus are compared. In some additional preferred embodiments, atleast the last CRISPR spacer (e.g., the last CRISPR spacer core) at the3′ end of the CRISPR locus and/or at least the first CRISPR spacer(e.g., the first CRISPR spacer core) at the 5′ end of the CRISPR locusare compared. In some further preferred embodiments, at least the firstCRISPR spacer (e.g., the first CRISPR spacer core) at the 5′ ends of theCRISPR loci is compared.

In some embodiments, the CRISPR loci comprise DNA, while in otherembodiments, the CRISPR loci comprise RNA. In some embodiments, thenucleic acid is of genomic origin, while in other embodiments, it is ofsynthetic or recombinant origin. In some embodiments, the CRISPR lociare double-stranded, while in other embodiments, they aresingle-stranded, whether representing the sense or antisense strand orcombinations thereof. In some embodiments, CRISPR loci are prepared byuse of recombinant DNA techniques (e.g., recombinant DNA), as describedherein.

In the context of the present invention, the CRISPR locus is orientedbased on the 5′-3′ orientation of the cas genes. The cas(CRISPR-associated) genes are usually neighbouring the CRISPR loci. Forexample, within the chromosome of S. thermophilus strain CNRZ1066, theCRISPR1 locus is located downstream to cas genes str0657, str0658,str0659, and str0660. The CRISPR1 locus is collinearly oriented to thecas genes. Thus, the cas genes are located upstream of CRISPR1. Thenon-coding sequence located between the stop codon of the last cas geneand the first nucleotide of the first CRISPR repeat is located upstreamto CRISPR and is referred to herein as the “CRISPR leader.” The CRISPRleader is located at the 5′end of the CRISPR locus. The non-codingsequence at the opposite side of the CRISPR locus is referred to hereinas the “CRISPR trailer.” The CRISPR trailer starts right after the lastnucleotide of the last CRISPR repeat. This last CRISPR repeat is alsoreferred to as a “terminal repeat.” The CRISPR trailer and terminalrepeats are located at the 3′ end of the CRISPR locus. For example,CRISPR1 leader in strain CNRZ1066 has sequence5′-CAAGGACAGTTATTGATTTTATAATCACTATGTGGGTATAAAAACGTCAAAATTTCATTTGA G-3′(SEQ ID NO:12), and the CRISPR trailer has the sequence5′-TTGATTCAACATAAAAAGCCAGTTCAATTGAACTMGCTTT-3′ (SEQ ID NO:13). TheCRISPR leader corresponds to positions 625038 to 625100, and the CRISPRtrailer corresponds to positions 627845 to 627885 in the genome of S.thermophilus CNRZ1066 (CP000024).

As used herein the term “portion thereof” in the context of a CRISPRlocus means at least about 10 nucleotides, about 20 nucleotides, about24 nucleotides, about 30 nucleotides, about 40 nucleotides, about 44nucleotides, about 50 nucleotides, about 60 nucleotides, about 70nucleotides, about 80 nucleotides, about 90 nucleotides, about 98nucleotides or even about 100 or more nucleotides (e.g., at least about44-98 nucleotides) of a CRISPR locus

In some further embodiments, the term “portion thereof” in the contextof a CRISPR locus means at least the first about 10 nucleotides, about20 nucleotides, about 24 nucleotides, about 30 nucleotides, about 40nucleotides, about 44 nucleotides, about 50 nucleotides, about 60nucleotides, about 70 nucleotides, about 80 nucleotides, about 90nucleotides, about 98 nucleotides, or about 100 or more nucleotides(e.g., at least about 44-98 nucleotides) downstream from the firstnucleotide of the first CRISPR repeat at the 5′ end of a CRISPR locus orupstream from the last nucleotide of the last CRISPR repeat at the 3′end of a CRISPR locus. In some preferred embodiments, the term “portionthereof” refers to the at least about the first 44 nucleotidesdownstream from the first nucleotide of the first CRISPR repeat at the5′ end of a CRISPR locus or at least about 44 nucleotides upstream fromthe last nucleotide of the last CRISPR repeat at the 3′ end of a CRISPRlocus.

In some embodiments, the minimum size of the duplicated sequence isabout 24 nucleotides and minimum size of the tagging sequence is about20 nucleotides. Thus, in some preferred embodiments, the term “portionthereof” in the context of a CRISPR locus, means at least 44nucleotides.

In some embodiments, the maximum size of the duplicated sequence isabout 40 nucleotides and the maximum size of the tagging sequence isabout 58 nucleotides. Thus, in some embodiments, the term “portionthereof” when used in the context of a CRISPR locus means at least about98 nucleotides. In some preferred embodiments, the term “portionthereof” in the context of a CRISPR locus means at least about 44-98nucleotides.

The present invention also provides CRISPR variants, as well as methodsfor generating CRISPR variants. In further embodiments, CRISPR variantsare isolated, cloned and/or sequenced using methods known in the art. Insome embodiments, CRISPR variants find use as targets for detectionand/or identification purposes, while in alternative embodiments, CRISPRvariants find use in engineering resistance against nucleic acidmolecules.

C. End of a CRISPR Locus

When comparing the CRISPR locus or a portion thereof from the parentbacterium and a tagged bacterium, at least about 10 nucleotides, about20 nucleotides, about 24 nucleotides, about 30 nucleotides, about 40nucleotides, about 44 nucleotides, about 50 nucleotides, about 60nucleotides, about 70 nucleotides, about 80 nucleotides, about 90nucleotides, about 98 nucleotides, or about 100 nucleotides (e.g., atleast about 44-98 nucleotides) of a CRISPR locus are compared. In somepreferred embodiments, at least about 10 nucleotides, about 20nucleotides, about 24 nucleotides, about 30 nucleotides, about 40nucleotides, about 44 nucleotides, about 50 nucleotides, about 60nucleotides, about 70 nucleotides, about 80 nucleotides, about 90nucleotides, about 98 nucleotides, or about 100 or more nucleotides(e.g., at least about 44-98 nucleotides) at one or both ends of a CRISPRlocus are compared.

In some preferred embodiments, at least the first about 10 nucleotides,about 20 nucleotides, about 24 nucleotides, about 30 nucleotides, about40 nucleotides, about 44 nucleotides, about 50 nucleotides, about 60nucleotides, about 70 nucleotides, about 80 nucleotides, about 90nucleotides, about 98 nucleotides or about 100 or more nucleotides(e.g., at least about 44-98 nucleotides) at the 5′ end of a CRISPR locusor at the 3′ end of a CRISPR locus are compared. In some preferredembodiments, at least the first about 44 nucleotides at the 5′ end of aCRISPR locus or the last about 44 nucleotides at the 3′ end of a CRISPRlocus are compared.

In some embodiments, at least the first about 10 nucleotides, about 20nucleotides, about 24 nucleotides, about 30 nucleotides, about 40nucleotides, about 44 nucleotides, about 50 nucleotides, about 60nucleotides, about 70 nucleotides, about 80 nucleotides, about 90nucleotides, about 98 nucleotides, or about 100 or more nucleotides(e.g., at least about 44-98 nucleotides) downstream from the firstnucleotide of the first CRISPR repeat at the 5′ end of a CRISPR locus orupstream from the last nucleotide of the last CRISPR repeat at the 3′end of a CRISPR locus are compared. In some preferred embodiments, atleast about the first 44 nucleotides downstream from the firstnucleotide of the first CRISPR repeat at the 5′ end of a CRISPR locus orabout at least 44 nucleotides upstream from the last nucleotide of thelast CRISPR repeat at the 3′ end of a CRISPR locus are compared.

In some embodiments, the minimum size of the duplicated sequence isabout 24 nucleotides and minimum size of the tagging sequence is about20 nucleotides. In some preferred embodiments, at least 44 nucleotidesare compared. In some alternative embodiments, the maximum size of theduplicated sequence is about 40 nucleotides and the maximum size of thetagging sequence is about 58 nucleotides. In some preferred embodiments,at least 98 nucleotides are compared. In some alternative preferredembodiments, at least about 44-98 nucleotides are compared.

D. CRISPR Repeat

As used herein, the term “CRISPR repeat” has the conventional meaning asused in the art (i.e., multiple short direct repeats, which show no orvery little sequence variation within a given CRISPR locus). As usedherein, in context, “CRISPR repeat” is synonymous with the term“CRISPR.”

A CRISPR locus comprises one or more CRISPR repeats than there areCRISPR spacers. Thus, the CRISPR repeat corresponds to the repeatedsequence within a CRISPR locus. For example, except for the terminalrepeat, the typical repeat sequence of the S. thermophilus CRISPR1sequence is:

(SEQ ID NO: 14) 5′-gtttttgtactctcaagatttaagtaactgtacaac-3′

Point variations of this repeat sequence have been observed for repeatsequences within a CRISPR locus of a given strain and for repeatsequences within a CRISPR locus of strains from a given species, butthey are very rare. Compared to this typical repeat sequence, theterminal repeat sequence of a given CRISPR locus always shows the samevariation at its 3′ end. Point variations of this terminal repeatsequence have also been observed but they are rare. CRISPR repeats maynaturally occur in the parent bacterium. GenBank accession numbers ofCRISPR1 sequences include: CP000023, CP000024, DQ072985, DQ072986,DQ072987, DQ072988, DQ072989, DQ072990, DQ072991, DQ072992, DQ072993,DQ072994, DQ072995, DQ072996, D0072997, DQ072998, DQ072999, DQ073000,DQ073001, DQ073002, DQ073003, DQ073004, DQ073005, DQ073006, DQ073007,DQ073008, and AAGS01000003.

As described in further detail herein, a duplicated sequence derived,derivable, obtained or obtainable from a parent bacterium. In somepreferred embodiments, the sequence comprises the genomic DNA of aparent bacterium. In some particularly preferred embodiments, theduplicated CRISPR repeat (e.g., in the same CRISPR locus) is integratediteratively, sequentially, simultaneously or substantiallysimultaneously along with the tagging sequence into the parent bacteriumto give rise to a tagged bacterium.

The number of nucleotides in a repeat is generally about 20 to about 40base pairs (e.g., about 36 base pairs). However, it is not intended thatthe present invention be limited any particular range within about 20and about 40 base pairs. Indeed, it is intended that every maximumnumerical limitation given throughout this specification includes everylower numerical limitation, as if such lower numerical limitations wereexpressly written herein. Every minimum numerical limitation giventhroughout this specification will include every higher numericallimitation, as if such higher numerical limitations were expresslywritten herein. Every numerical range given throughout thisspecification will include every narrower numerical range that fallswithin such broader numerical range, as if such narrower numericalranges were all expressly written herein.

In additional embodiments, the number of repeats range from about 1 toabout 250. However, it is not intended that the present invention belimited any particular range within about 1 and about 250 repeats.Indeed, as indicated above, it is intended that every maximum numericallimitation given throughout this specification includes every lowernumerical limitation, as if such lower numerical limitations wereexpressly written herein. Every minimum numerical limitation giventhroughout this specification will include every higher numericallimitation, as if such higher numerical limitations were expresslywritten herein. Every numerical range given throughout thisspecification will include every narrower numerical range that fallswithin such broader numerical range, as if such narrower numericalranges were all expressly written herein. Indeed, it is intended thatthis apply to all numerical ranges provided herein.

In some embodiments, the CRISPR repeats comprise DNA, while in otherembodiments, the CRISPR repeats comprise RNA. In some embodiments, thenucleic acid is of genomic origin, while in other embodiments, it is ofsynthetic or recombinant origin. In some embodiments, the CRISPR repeatgenes are double-stranded or single-stranded whether representing thesense or antisense strand or combinations thereof. In some embodiments,CRISPR repeat genes are prepared by use of recombinant DNA techniques(e.g., recombinant DNA), as described herein.

In some embodiments, one or more of the CRISPR repeats are used toengineer a cell (e.g., a recipient cell). For example, in someembodiments, the CRISPR repeat(s) are inserted into the DNA of a cell(e.g., plasmid and/or genomic DNA of a recipient cell), using anysuitable method known in the art. In additional embodiments, the CRISPRrepeat(s) find use as a template upon which to modify (e.g., mutate) theDNA of a cell (e.g., plasmid and/or genomic DNA of a recipient cell),such that CRISPR repeat(s) are created or engineered in the DNA of thecell. In additional embodiments, the CRISPR repeat(s) are present in atleast one construct, at least one plasmid, and/or at least one vector,etc. In further embodiments, the CRISPR repeats are introduced into thecell using any suitable method known in the art.

In some further embodiments, one or more cas genes or proteins are usedtogether with or in combination with one or more, preferably, two ormore CRISPR repeats and optionally one or more CRISPR spacers. In someparticularly preferred embodiments, the cas gene(s) or protein(s) andCRISPR repeat(s) form a functional combination as described below.

E. CRISPR Spacer

As used herein, “CRISPR spacer” encompasses non-repetitive spacersequences that are located between repeats (i.e., CRISPR repeats) ofCRISPR loci. In some embodiments of the present invention, a “CRISPRspacer” refers to the nucleic acid segment that is flanked by two CRISPRrepeats. It has been found that CRISPR spacer sequences often havesignificant similarities to a variety of mobile DNA molecules (e.g.,bacteriophages and plasmids). In some preferred embodiments, CRISPRspacers are located between two identical CRISPR repeats. In someembodiments, CRISPR spacers are identified by sequence analysis of theDNA stretches located in between two CRISPR repeats.

Interestingly, cells carrying these CRISPR spacers have been foundunable to be infected by DNA molecules containing sequences homologousto the spacers (Mojica et al. [2005], supra). In most embodiments, theCRISPR spacer is naturally present between two identical multiple shortdirect repeats that are palindromic.

In some embodiments, the CRISPR spacer is homologous to the targetnucleic acid or a transcription product thereof or an identifiedsequence. Although in some embodiments, homology is taken intoconsideration in terms of similarity, in the context of the presentinvention, in some preferred embodiments, homology is expressed in termsof sequence identity. In preferred embodiments, analysis of homologoussequences includes a CRISPR spacer, which in some embodiment is at leastabout 70, about 75, about 80, about 85, about 90%, about 91%, about 92%,about 93%, about 94%, about 95%, about 96%, about 97%, about 98% orabout 99% identical to the target nucleic acid sequence or atranscription product thereof or an identified sequence (e.g., asequence of interest). In some embodiments, the CRISPR spacer is 100%identical to the target nucleic acid sequence.

The number of CRISPR spacers at a given CRISPR loci or locus can varybetween species. In some preferred embodiments, the number of spacersranges from about 1 to about 248. However, it is not intended that thepresent invention be limited any particular range within about 1 andabout 140 spacers. Indeed, as indicated above, it is intended that everymaximum numerical limitation given throughout this specificationincludes every lower numerical limitation, as if such lower numericallimitations were expressly written herein. Every minimum numericallimitation given throughout this specification will include every highernumerical limitation, as if such higher numerical limitations wereexpressly written herein. Every numerical range given throughout thisspecification will include every narrower numerical range that fallswithin such broader numerical range, as if such narrower numericalranges were all expressly written herein. Indeed, it is intended thatthis apply to all numerical ranges provided herein.

In some embodiments, CRISPR spacers are identified by sequence analysisas the DNA stretches located between two repeats.

As described herein, the present invention provides methods andcompositions that facilitate the use of one or more cas genes orproteins in combination with one or more, preferably, two or more CRISPRrepeats suitable to confer specificity of immunity to at least oneCRISPR spacer in a recipient cella In some preferred embodiments, atleast one cas genes or proteins and at least one CRISPR repeat are usedin functional combinations to confer specificity of immunity to at leastone CRISPR spacer in a cell.

As used herein, the term “specificity of immunity” means that immunityis conferred against a specific nucleic acid sequence or transcriptionproduct thereof, using a specific CRISPR spacer or pseudo-CRISPR spacersequence. As indicated herein, a given CRISPR spacer does not conferresistance against any nucleic acid sequence or transcription productthereof but only to those sequences against which the CRISPR spacer orpseudo-CRISPR spacer is homologous (e.g., those that are 100%identical).

In some embodiments, the CRISPR spacer(s) are obtained from a donororganism that is different from the recipient cell. In some preferredembodiments, the donor and recipient cells are different bacterialstrains, species, and/or genera. In some preferred embodiments, the atleast one cas genes or proteins and/or at least one CRISPR repeats areobtained from a different organism than the recipient organism. In somepreferred embodiments, at least two CRISPR repeats are transferred. Insome preferred embodiments, the CRISPR spacers are obtained from anorganism that is heterologous to the recipient or a further donor cellfrom which the at least one cas genes and/or proteins, and/or at leastone CRISPR repeat are obtained. In some alternative preferredembodiments, the CRISPR spacers are obtained from an organism that ishomologous to the recipient or a further donor cell from which the atleast one cos genes and/or proteins, and/or at least one CRISPR repeatare obtained. In some preferred embodiments, the CRISPR spacer(s) is/aredesigned and produced using recombinant methods known in the art.Indeed, it is intended that the CRISPR spacers be produced using anysuitable method known in the art.

In some embodiments, the CRISPR spacers are heterologous to therecipient cell from which at least one cas genes or proteins and/or theat least one (in some embodiments, preferably, two or more) CRISPRrepeats are obtained. In some alternative embodiments, the CRISPRspacers are homologous to the recipient cell from which at least one casgenes or proteins and/or the at least one (in some embodiments,preferably, two or more) CRISPR repeats are obtained. Indeed, it isintended that any of the elements utilized in the methods beheterologous or homologous. In some embodiments, where multiple elementsare used (e.g., any combination of CRISPR spacer(s), CRISPR repeat(s),cas gene(s), and Cas protein(s)), some elements are homologous with eachother and some elements are heterologous to each other (e.g., in someembodiments, the CRISPR spacer(s) and cas genes are homologous, but theCRISPR repeat(s) is/are heterologous). Thus, in some embodiments, theCRISPR spacer is not naturally associated with the CRISPR repeat and/orcas genes and/or functional CRISPR repeat-cas gene combination. Indeed,it is intended that any combination of heterologous and homologouselements find use in the present invention. In yet additionalembodiments, the donor and recipient cells are heterologous, while infurther embodiments, they are homologous. It is also intended that theelements contained within the donor and recipient cells be homologousand/or heterologous. The elements (e.g., CRISPR spacers) are introducedinto plasmid and/or genomic DNA of the recipient cell utilizing anysuitable method known in the art.

In some preferred embodiments, at least one CRISPR spacer is used toengineer a cell (e.g., a recipient cell). In further embodiments, CRISPRspacers are used as a template upon which to modify (e.g., mutate) theplasmid and/or genomic DNA of a cell (e.g., a recipient cell), such thatCRISPR spacers are created in the DNA of the cell. In some embodiments,the CRISPR spacer(s) is/are cloned into at least one construct, plasmidor other vector, with which the recipient cell is then transformed,using any suitable method known in the art. CRISPR spacers are flankedby two CRISPR repeats (i.e., a CRISPR spacer has at least one CRISPRrepeat on each side).

Although it is not intended that the present invention be limited to anyparticular mechanism, theory nor hypothesis, it is contemplated that thefurther a given CRISPR spacer is from the 5′ end of the CRISPR locuscomprising the cas gene(s) and/or the leader sequence, the lower theresistance conferred by that CRISPR spacer is. Thus, in some embodimentsof the present invention, one or more of the first 100 CRISPR spacersfrom the 5′ end of the CRISPR locus are modified, in other embodiments,one or more of the first 50 CRISPR spacers from the 5′ end of the CRISPRlocus are modified, in additional embodiments, one or more of the first40 CRISPR spacers from the 5′ end of the CRISPR locus are modified, instill further embodiments, one or more of the first 30 CRISPR spacersfrom the 5′ end of the CRISPR locus are modified, in yet additionalembodiments, one or more of the first 20 CRISPR spacers from the 5′ endof the CRISPR locus are modified, in still more embodiments, one or moreof the first 15 CRISPR spacers from the 5′ end of the CRISPR locus aremodified, and in some preferred embodiments, one or more of the first 10CRISPR spacers from the 5′ end of the CRISPR locus are modified. Asindicated herein, different bacteria have different numbers of CRISPRspacers, thus in some embodiments various spacers are modified.

F. CRISPR Spacer Core

In some embodiments, for a specific CRISPR type within a microbialspecies, the CRISPR spacer is represented by a defined predominantlength, although the size may vary. CRISPR types described to date havebeen found to contain a predominant spacer length of between about 20 bpand about 58 bp.

As used herein, the term “CRISPR spacer core” refers to the length ofthe shortest observed spacer within a CRISPR type. Thus, for example,within S. thermophilus CRISPR1 , the dominant spacer length is 30 bp,with a minority of spacers between 28 bp and 32 bp in size. Thus, in S.thermophilus CRISPR1, the CRISPR spacer core is defined as a continuousstretch of 28 bp.

In some preferred embodiments of the present invention, the CRISPRspacer core is homologous to the target nucleic acid, a transcriptionproduct thereof, or an identified sequence over the length of the coresequence. Although homology can also be considered in terms ofsimilarity, in some preferred embodiments of the present invention,homology is expressed in terms of sequence identity. Thus, in someembodiments, a homologous sequence encompasses a CRISPR spacer core,which may be at least about 90% identical, or at least about 91, about92, about 93, about 94, about 95, about 96, about 97, about 98 or about99% identical to the target nucleic acid sequence, a transcriptionproduct thereof, or an identified sequence over the length of the coresequence. In some particularly preferred embodiments, the CRISPR spacercore is 100% identical to the target nucleic acid sequence,transcription product thereof, or an identified sequence over the lengthof the core sequence.

During the development of the present invention, the CRISPR sequences ofvarious S. thermophilus strains, including closely related industrialstrains and phage-resistant variants were analyzed. Differences in thenumber and type of spacers were observed primarily at the CRISPR1 locus.Notably, phage sensitivity appeared to be correlated with CRISPR1 spacercontent. Specifically, the spacer content was nearly identical betweenparental strains and phage-resistant derivatives, except for additionalspacers present in the latter. These findings suggested a potentialrelationship between the presence of additional spacers and thedifferences observed in the phage sensitivity of a given strain. Thisobservation prompted the investigation of the origin and function ofadditional spacers present in phage-resistant mutants.

G. Pseudo-CRISPR Spacer

As used herein, the terms “pseudo-CRISPR spacer,” “pro-spacer,” and“proto-spacer” refer to a nucleic acid sequence present in an organism(e.g., a donor organism, including but not limited to bacteriophage),which is preferably essential for function and/or survival and/orreplication and/or infectivity, etc., and which forms a CRISPR spacersequence. In some embodiments, the pseudo-CRISPR spacers find use inproducing CRISPR spacer sequences that are complementary to orhomologous to the pseudo-CRISPR spacer.

In some embodiments, at least one pseudo-CRISPR spacers and CRISPRspacer(s) that is/are complementary or homologous to at least onepseudo-CRISPR spacer(s) are used to engineer a recipient cell. In someembodiments, the pseudo-CRISPR spacers or CRISPR spacer(s) that is/arecomplementary or homologous to the one or more pseudo-CRISPR spacer(s)are inserted into the plasmid and/or genomic DNA of a recipient cellusing any suitable method known in the art.

In some additional embodiments, the pseudo-CRISPR spacers are used as atemplate upon which to modify (e.g., mutate) the plasmid and/or genomicDNA of a recipient cell, such that CRISPR spacers are created in theplasmid and/or genomic DNA of the cell. In some further embodiments, thepseudo-CRISPR spacers or CRISPR spacer(s) that is/are complementary orhomologous to the one or more pseudo-CRISPR spacer(s) are cloned into aconstruct, plasmid and/or vector, etc. is/are introduced into the hostcell using any suitable method known in the art.

H. Cas Proteins and cas Genes

As used herein, the term “cas gene” has the conventional meaning as usedin the art and refers to one or more car genes that are generallycoupled, associated or close to or in the vicinity of flanking CRISPRloci.

A comprehensive review of the Cas protein family is presented by Haft etal. (Haft et al., Comput. Biol., 1, 6 e60 [2005]). As described therein,41 CRISPR-associated (cas) gene families are described, in addition tothe four previously known gene families. As indicated, CRISPR systemsbelong to different classes, with different repeat patterns, sets ofgenes, and species ranges. Indeed, the number of cas genes at a givenCRISPR locus can vary between species.

In some embodiments, one or more of the cas genes and/or proteinsnaturally occur in a recipient cell and one or more heterologous spacersis/are integrated or inserted in the CRISPR loci adjacent to the one ormore of the cas genes or proteins.

In some embodiments, one or more of the cas genes and/or proteins is/areheterologous to the recipient cell and one or more of the spacers is/arehomologous or heterologous. In some preferred embodiments, the spacersare integrated or inserted in the CRISPR loci adjacent to the one ormore of the cas gene or proteins.

CRISPR loci are typically found in the vicinity of four genes named cas1to cas4. The most common arrangement of these genes iscas3-cas4-cas1-cas2. The Cas3 protein appears to be a helicase, whereasCas4 resembles the RecB family of exonucleases and contains acysteine-rich motif, suggestive of DNA binding. Cas1 is generally highlybasic and is the only Cas protein found consistently in all species thatcontain CRISPR loci. Cas2 remains to be characterized. cas1-4 aretypically characterized by their close proximity to the CRISPR loci andtheir broad distribution across bacterial and archaeal species. Althoughnot all cas1-4 genes associate with all CRISPR loci, they are all foundin multiple subtypes.

In addition, there is another cluster of three genes associated withCRISPR structures in many bacterial species, named here as cas1B, cas5and cas6 (See, Bolotin et al., [2005], supra). In some embodiments, thecas gene is selected from cas1, cas2, cas3, cas4, cas1B, cas5 and/orcas6. In some embodiments, the cas gene is cas1. In yet otherembodiments, the cas gene is selected from cas1, cas2, cas3, cas4,cas1B, cas5 and/or cas6 fragments, variants, homologues and/orderivatives thereof. In some additional embodiments, a combination oftwo or more cas genes find use, any suitable combination. It is notedthat the nomenclature of the cas genes is in flux. Thus, the text hereinmust be taken in context.

The term “Cas protein” also encompasses a plurality of Cas proteins(e.g., between about 2 and about 12 Cas proteins, more preferably,between about 3 and about 11 Cas proteins, more preferably, betweenabout 4 and about 10 Cas proteins, more preferably, between about 4 andabout 9 Cas proteins, more preferably, between about 4 and about 8 Casproteins, and more preferably, between about 4 and about 7 proteinsgenes; such as 4, 5, 6, or 7 Cas proteins).

In some embodiments, the Cas proteins are encoded by cas genescomprising DNA, while in other embodiments, the cas comprise RNA. Insome embodiments, the nucleic acid is of genomic origin, while in otherembodiments, it is of synthetic or recombinant origin. In someembodiments, the cas genes encoding the Cas proteins are double-strandedor single-stranded whether representing the sense or antisense strand orcombinations thereof. In some embodiments, cas genes are prepared by useof recombinant DNA techniques (e.g., recombinant DNA), as describedherein. U.S. Provisional Appln. Ser. No. 60/907,721, filed Mar. 3,2007,incorporated herein by reference in its entirety.

I. Bacteriophage

As used herein, the term “bacteriophage” (or “phage”) has itsconventional meaning as understood in the art (i.e., a virus thatselectively infects one or more bacterial species). Many bacteriophagesare specific to a particular genus or species or strain of bacteria. Insome preferred embodiments, the phages are capable of infecting parentbacteria and/or host cells. In some embodiments, bacteriophages arevirulent to the parent bacterium. In some embodiments, the phage arelytic, while in other embodiments, the phage are lysogenic.

A lytic bacteriophage is one that follows the lytic pathway throughcompletion of the lytic cycle, rather than entering the lysogenicpathway. A lytic bacteriophage undergoes viral replication leading tolysis of the cell membrane, destruction of the cell, and release ofprogeny bacteriophage particles capable of infecting other cells.

A lysogenic bacteriophage is one capable of entering the lysogenicpathway, in which the bacteriophage becomes a dormant, passive part ofthe cell's genome through prior to completion of its lytic cycle.

Bacteriophages that find use in the present invention include, but arenot limited to bacteriophages that belong to any of the following virusfamilies: Corticoviridae, Cystoviridae, lnoviridae, Leviviridae,Microviridae, Myoviridae, Podoviridae, Siphoviridae, or Tectiviridae. Insome embodiments, bacteriophage that infect bacteria that are pathogenicto plants and/or animals (including humans) find particular use.

In some particularly preferred embodiments, the bacteriophage of thepresent invention include, but are not limited to, those bacteriophagecapable of infecting a bacterium that naturally comprises one or moreCRISPR loci. CRISPR loci have been identified in more than 40prokaryotes (See e.g., Jansen et al., Mol. Microbiol., 43:1565-1575[2002]; and Mojica et al., [2005]) including, but not limited toAeropyrum, Pyrobaculum, Sulfolobus, Archaeoglobus, Halocarcula,Methanobacterium, Methanococcus, Methanosarcina, Methanopyrus,Pyrococcus, Picrophilus, Thermoplasma, Corynebacterium, Mycobacterium,Streptomyces, Aquifex, Porphyromonas, Chlorobium, Thermus, Bacillus,Listeria, Staphylococcus, Clostridium, Thermoanaerobacter, Mycoplasma,Fusobacterium, Azarcus, Chromobacterium, Neisseria, Nitrosomonas,Desulfovibrio, Geobacter, Myxococcus, Campylobacter, Wolinella,Acinetobacter, Erwinia, Escherichia, Legionella, Methylococcus,Pasteurella, Photobacterium, Salmonella, Xanthomonas, Yersinia,Treponema, and Thermotoga.

In some embodiments, the bacteriophage include, but are not limited to,those bacteriophage capable of infecting bacteria belonging to thefollowing genera: Escherichia, Shigella, Salmonella, Erwinia, Yersinia,Bacillus, Vibrio, Legionella, Pseudomonas, Neisseria, Bordetella,Helicobacter, Listeria, Agrobacterium, Staphylococcus, Streptococcus,Enterococcus, Clostridium, Corynebacterium, Mycobacterium, Treponema,Borrelia, Francisella , Brucella and Xanthomonas.

In yet additional embodiments, the bacteriophage include, but are notlimited to, those bacteriophage capable of infecting (or transducing)lactic acid bacteria, Bifidobacterium, Brevibacterium,Propionibacterium, Lactococcus, Streptococcus, Lactobacillus (e.g., L.acidophilus), Enterococcus, Pediococcus, Leuconostoc, and Oenococcus.

In still further embodiments, the bacteriophage include, but are notlimited to, those bacteriophage capable of infecting Lactococcus lactis(e.g., L. lactis subsp. lactis and L. lactis subsp. cremoris, and L.lactis subsp. lactis biovar diacetylactis), Streptococcus thermophiles,Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus helveticus,Bifidobacterium lactis, Lactobacillus acidophilus, Lactobacillus casei,Bifidobacterium infantis, Lactobacillus paracasei, Lactobacillussalivarius, Lactobacillus plantarum, Lactobacillus reuteri,Lactobacillus gasseri, Lactobacillus johnsonii or Bifidobacteriumlongum.

In some particularly preferred embodiments, the bacteriophages include,but are not limited to, those bacteriophages capable of infectingbacteria that comprise one or more heterologous CRISPR loci. In someembodiments, the bacteria comprise one or more heterologous CRISPR loci,and/or one or more heterologous cas genes, and/or one or moreheterologous CRISPR repeats, and/or one or more heterologous CRISPRspacers.

Infection of bacteria by phage results from the injection or transfer ofphage DNA into cells. In some embodiments, infection leads to expression(i.e., transcription and translation) of the bacteriophage nucleic acidwithin the cell and continuation of the bacteriophage life cycle. Insome embodiments involving recombinant bacteriophage, recombinantsequences within the phage genome (e.g., reporter nucleic acids), arealso expressed.

It has been found that CRISPR spacer sequences in prokaryotes often havesignificant similarities to a variety of DNA molecules, including suchgenetic elements as chromosomes, bacteriophages, and conjugativeplasmids. It has been reported that cells carrying these CRISPR spacersare unable to be infected by DNA molecules containing sequenceshomologous to the spacers (See, Mojica et al., [2005]).

In some embodiments of the present invention, the parent bacteria areexposed (e.g., iteratively, sequentially, simultaneously orsubstantially simultaneously) to more than one bacteriophage. In somepreferred embodiments, the bacteria are exposed to mixtures of one ormore (e.g., several) different phages. In some alternative preferredembodiments, the parent bacteria are sensitive to each of thebacteriophages to which they are exposed.

In some embodiments, each of the tagging sequences from each of thebacteriophages and/or each of the duplicated sequences (e.g., theduplicated CRISPR repeat) from the parent bacterium integrate into thesame CRISPR locus. In other embodiments, each of the tagging sequencesand/or each of the duplicated sequences integrate at one or both ends ofthe same CRISPR locus. In yet additional embodiments, each of thetagging sequences and/or each of the duplicated sequences integrate atthe 5′ and/or the 3′ end of the same CRISPR locus. In some preferredembodiments, each of the tagging sequences and/or each of the duplicatedsequences integrate at the 5′ end of the same CRISPR locus.

In some embodiments, each of the tagging sequences and/or each of theduplicated sequences from the parent bacteria integrate iteratively,simultaneously or substantially simultaneously. In embodiments in whicheach of the tagging sequences and/or each of the duplicated sequencesare integrated sequentially, the first tagging sequence and/or the firstduplicated sequence is integrated into the parent bacteria. A secondtagging sequence from a second bacteriophage and/or another duplicatedsequence are then integrated into the parent bacterium. In somepreferred embodiments, the tagging sequence and/or the duplicatedsequence integrate into the chromosomal DNA of the parent bacteria.

In some embodiments, each of the tagging sequences and/or each of theduplicated sequences integrate into one end (e.g., the 5′ end) of thesame CRISPR locus adjacent (i.e., next to) each other. Thus, in someembodiments, each of the tagging sequences and/or duplicated sequencesintegrate sequentially, whereby the first sequences are integrated intothe parent bacterium at one end (e.g., within or at the 5′ and/or the 3′end) of the CRISPR locus. In some preferred embodiments, a secondtagging sequence and/or duplicated sequence is then integrated into theparent bacteria adjacent (e.g., directly adjacent) to the first pair ofsequences. In some embodiments, the second sequences integrate into theparent bacterium adjacent (e.g., directly adjacent) to the 5′ or the 3′end of the first sequences. In some preferred embodiments, the secondsequences integrate into the parent bacterium adjacent (e.g., directlyadjacent) to the 3′ end of the first sequences. In embodiments in whichadditional sequences are provided, these are then integrated.

In some embodiments, each of the sequences integrate adjacent (i.e.,next to) each other within or at the 3′ end and/or at the 5′ end of thesame CRISPR locus of the parent bacteria. In some preferred embodiments,each of the sequences integrate adjacent (i.e., next to) each other atthe 5′ end of the same CRISPR locus of the parent bacteria. In someparticularly preferred embodiments, each of the sequences integrateadjacent (i.e., next to) each other upstream of the 5′ end of the CRISPRlocus of the parent bacteria. In some alternatively preferredembodiments, each of the sequences integrate adjacent (i.e., next to)each other, in a location that is upstream of the 5′ CRISPR repeat ofthe CRISPR locus of the parent bacteria. In some more particularlypreferred embodiments, each of the sequences integrate adjacent (i.e.,next to) each other upstream of the first 5′ CRISPR repeat of the CRISPRlocus of the parent bacterium.

J. Parent Bacteria

As used herein the terms “parent bacterium” “parent bacteria” and“parental strain” refer to any bacterium/bacteria/strains that is/areexposed to one or more virulent bacteriophage. In some particularlypreferred embodiments, the parent bacteria are sensitive to the virulentphage. In some preferred embodiments, the parental strain is infected bythe bacteriophage. In some particularly preferred embodiments, theinfection by phage renders the parent bacterium/bacteria/strain or asubpopulation thereof insensitive to further infection by thebacteriophage. In some preferred embodiments, the infection of a “parentbacterium” by one or more bacteriophage results in the creation of atagged strain that can be selected based on its insensitivity to thebacteriophage. In some preferred embodiments, “bacteriophage resistantmutant” are bacteria that are tagged or tagged according to the methodsof the present invention. In some embodiments, the parent bacteria arewild-type bacterial strains. In some preferred embodiments, the parentbacteria are wild-type strains of bacteria that have not been previouslyinfected with any bacteriophage. In some preferred embodiments, theparent bacteria are wild-type strains of bacteria that have not beenpreviously tagged, while in some alternative embodiments, the patentbacteria are bacteriophage resistant mutants that have been previouslytagged.

In some particularly preferred embodiments, the parent bacterium isselected from any bacterium that naturally comprises one or more CRISPRloci. CRISPR loci have been identified in more than 40 prokaryotes(Jansen et al. [2002) supra; Mojica et al., [2005], supra; and Haft etal., [2005], supra) including, but not limited to Aeropyrum,Pyrobaculum, Sulfolobus, Archaeoglobus, Halocarcula, Methanobacterium,Methanococcus, Methanosarcina, Methanopyrus, Pyrococcus, Picrophilus,Thermoplasma, Corynebacterium, Mycobacterium, Streptomyces, Aquifex,Porphyromonas, Chlorobium, Thermus, Bacillus, Listeria, Staphylococcus,Clostridium, Thermoanaerobacter, Mycoplasma, Fusobacterium, Azarcus,Chromobacterium. Neisseria, Nitrosomonas, Desulfovibrio, Geobacter,Myxococcus, Campylobacter, Wolinella, Acinetobacter, Erwinia,Escherichia, Legionella, Methylococcus, Pasteurella, Photobacterium,Salmonella, Xanthomonas, Yersinia, Treponema and Thermotoga.

In some embodiments, the parent bacterium comprises one or moreheterologous CRISPR spacers, one or more heterologous CRISPR repeats,and/or one or more heterologous cas genes. In some alternativeembodiments, the parent bacterium comprises one or more heterologousCRISPR loci, preferably, one or more complete CRISPR loci. In somefurther embodiments, the parent bacterium naturally comprises one ormore CRISPR loci and also comprises one or more heterologous CRISPRspacers, one or more heterologous CRISPR repeats, and/or one or moreheterologous cas genes. In some additional embodiments, the parentbacterium naturally comprises one or more CRISPR loci and also comprisesone or more heterologous CRISPR loci, preferably, one or more completeCRISPR loci.

In some preferred embodiments, the phage-resistant subpopulation createdby exposure of the parent bacteria to at least one phage is a pureculture. However, it is not intended that the present invention belimited to pure cultures of bacterial strains, variants, or phage.Indeed, it is intended that the present invention encompasses mixedcultures of cells and phage. In some embodiments, the mixed culture is amix of different mutants corresponding to different integration eventsat the same and/or at different CRISPR loci.

Although it is not intended that the present invention be so limited,preferred parental bacterial genera are Streptococcus and Lactobacillus.Indeed, it is intended that any bacterial species will find use in thepresent invention, including but not limited to Escherichia, Shigella,Salmonella, Erwinia, Yersinia, Bacillus, Vibrio, Legionella,Pseudomonas, Neisseria, Bordetella, Helicobacter, Listeria,Agrobacterium, Staphylococcus, Streptococcus, Enterococcus, Clostridium,Corynebacterium, Mycobacterium, Treponema, Borrelia, Francisella,Brucella, Bifidobacterium, Brevibacterium, Propionibacterium,Lactococcus, Lactobacillus, Enterococcus, Pediococcus, Leuconostoc,Oenococcus, and/or Xanthomonas. In some embodiments, the parent bacteriaare or are derived from lactic acid bacteria, including but not limitedto Bifidobacterium, Brevibacterium, Propionibacterium, Lactococcus,Streptococcus, Lactobacillus (e.g., L. acidophilus), Enterococcus,Pediococcus, Leuconostoc, and/or Oenococcus. In further embodiments, theparent bacteria are or are derived from Lactococcus lactis (e.g., L.lactis subsp. lactis and L. lactis subsp. cremoris, and L. lactis subsp.lactis biovar diacetylactis), L. delbrueckii subsp. bulgaricus, L.helveticus, L. acidophilus, L. casei, L. paracasei, L. salivarius, L.plantarum, L. reuteri, L. gasseri, L. johnsonii, Bifidobacterium lactis,B. infantis, B. longum, and/or Streptococcus thermophilus.

In embodiments of the present invention, the parent bacterium is a“food-grade bacterium” (i.e., a bacterium that is used and generallyregarded as safe for use in the preparation and/or production of foodand/or feed). In some preferred embodiments, the parent bacterium issuitable for use as a starter culture, a probiotic culture, and/or adietary supplement. In additional embodiments, the parent bacteriumfinds use in the fermentation of meat (e.g., beef, pork, lamb, andpoultry) including, but not limited to, lactic acid bacteria,Pediococcus cerevisiae, Lactobacillus plantarum, L. brevis, L. sakei, L.curvatus, Micrococcus species, Pediococcus pentosaceus, Staphylococcusxylosus, S. vitulinus and mixtures thereof (See e.g., Knorr (ed.), FoodBiotechnology, at 538-39 [1987]; and Pederson, Microbiology of FermentedFoods, at 210-34, 2d ed., [1979]; and U.S. Pat. No. 2,225,783, hereinincorporated by reference in its entirety). In yet additionalembodiments, he parent bacterium finds use in the fermentation ofvegetables (e.g., carrots, cucumbers, tomatoes, peppers, and cabbage)including, but not limited to, L. plantatum, L. brevis, Leuconostocmesenteroides, Pediococcus pentosaceus, and mixtures thereof (See e.g.,Knorr, supra; Pederson, supra; and U.S. Pat. Nos. 3,024,116, 3,403,032,3,932,674, and 3,897,307). In yet further embodiments, the parentbacterium finds use in the fermentation of dough formed from cereals(e.g., wheat, rye, rice, oats, barley, and corn). In still furtherembodiments, the parent bacterium finds use in the production of winethrough fermentation of fruit juice (e.g., grape juice). In someadditional embodiments, parent bacterium finds use in the fermentationof milk (e.g., L. delbrueckii subsp. bulgaricus, L. acidophilus, S.thermophilus, and mixtures thereof (See, Knorr, supra; and Pedersonsupra, at pages 105-35). In some preferred embodiments, the parentbacterium find use in the production of cheese, including but notlimited to L. delbrueckii subsp. bulgaricus. L. helveticus, L. lactissubsp. lactis, L lactis subsp. cremoris, L. lactis subsp. lactis biovardiacetylactis, S. thermophilus, Bifidobacterium Enterococcus, etc., andmixtures thereof (See e.g., Knorr, supra, and Pederson, supra, at135-51). In yet further embodiments, the parent bacterium finds use inthe fermentation of eggs, including but not limited to Pediococcuspentosaceus, Lactobacillus plantarum, and mixtures thereof (See, Knorr,supra). In some embodiments, the parent bacterium is finds use infermentation to produce various products, including but not limited tocheddar and cottage cheese (e.g., L. lactis subsp. lactis, L. lactissubsp. cremoris), yogurt (L. delbrueckii subsp. bulgaricus, and S.thermophilus), Swiss cheese (e.g., S. thermophilus, L. lactis, and L.helveticus), blue cheese (Leuconostoc cremoris), Italian cheese (L.bulgaricus and S. thermophilus), viili (L. lactis subsp. cremoris, L.lactis subsp. lactis biovar diacetylactis, Leuconostoc cremoris), yakult(L. casei), casein (L. lactis subsp. cremoris), natto (Bacillus subtilisvar. natto), wine (Leuconostoc oenos), sake (Leuconostoc mesenteroides),polymyxin (Bacillus polymyxa), colistin (Bacillus colistrium),bacitracin (Bacillus licheniformis), L-Glutamic acid (Brevibacteriumlactofermentum and Microbacterium ammoniaphilum), and acetone andbutanol (Clostridium acetobutyricum, and Clostridiumsaccharoperbutylacetonicum). In some preferred embodiments, the parentbacterial species are selected from S. thermophilus, L. delbrueckiisubsp. bulgaricus and/or L. acidophilus.

In yet additional embodiments, the parent bacteria find use in methodsincluding but not limited to antibiotic production, amino acidproduction, solvent production, and the production of other economicallyuseful materials. In still other embodiments the parent bacteria finduse in cosmetic, therapeutic, and/or pharmaceutical compositions. Insome embodiments the compositions have particular activities, includingbut not limited to regenerating the skin, including but not limited toanti-wrinkle properties, erasing old scars, repairing burn-damagedtissues, promoting skin healing, eliminating pigmentary spots, etc. Insome embodiments, the compositions either promote or inhibit the growthof nails, hair or hairs. In some additional embodiments, thecompositions comprise at least one microbial culture and/or taggedbacterium and/or a cell culture produced using the methods andcompositions of the present invention

In further embodiments, the parent bacteria are bacteriophageinsensitive mutants. Thus, in some embodiments, the parent bacteria areinsensitive to one or more bacteriophage. In some preferred embodiments,the parent bacterium is not a bacteriophage insensitive mutant for thebacteriophage that it is to be exposed to during use of the presentinvention.

K. Tagging Sequence

As used herein, the term “tagging sequence” refers to the portion of an“additional repeat-spacer unit” that is derived, derivable, obtained orobtainable from the genome of one or more bacteriophage(s)) that theparent bacterium is exposed to in accordance with the methods of thepresent invention and is used as a label or a tag (e.g., a unique labelor a unique tag). In some preferred embodiments, the tagging sequence isat least about 20 nucleotides in length, while in some more preferredembodiments, the tagging sequence is from about 20 to about 58nucleotides in length. However, in some alternative embodiments, a “tag”is generated using genetic elements from sources other than phage. Forexample, in some embodiments, the tag is provided by plasmids,transposable elements, isolated nucleic acid, etc. Indeed, in someembodiments, the tag is a unique, synthetic, non-functional sequence.Thus, it is not intended that the present invention be limited tonucleic acid tags that are generated solely from phage nucleic acid.

The tagging sequence is typically a sequence that is a naturallyoccurring sequence in the bacteriophage. Preferably, the taggingsequence has at least about 90%, about 95%, about 96%, about 97%, about98%, or about 99% identity to the naturally occurring sequence in thebacteriophage (e.g., the genome of the bacteriophage from which it isderived, derivable, obtained or obtainable). In some highly preferredembodiments, the tagging sequence has 100% identity to the naturallyoccurring sequence in the bacteriophage(e.g., the genome of thebacteriophage from which it is derived, derivable, obtained orobtainable).

In some embodiments, the tagging sequence has less than about 40%, about30%, about 20%, about 10%, about 5%, about 4%, about 3%, about 2%, about1% or about 0% identity to any other CRISPR spacers or CRISPR spacercores in the one or more CRISPR loci of the tagged bacterium. In someembodiments, the tagging sequence has less than about 40%, about 30%,about 20%, about 10%, about 5%, about 4%, about 3%, about 2%, about 1%,or about 0% identity to any other sequence in the one or more CRISPRloci of the tagged bacterium.

In some alternative embodiments, the tagging sequence is a sequence thatis identical to a sequence (e.g., a CRISPR spacer) in the CRISPR locusof the bacterium. In some alternative embodiments, the tagging sequenceis a sequence that is almost identical to a sequence (e.g., a CRISPRspacer) in the CRISPR locus of the bacterium in that it contains one ormore single nucleotide polymorphisms (e.g., one or two single nucleotidepolymorphisms).

In some embodiments, at least one tagging sequence is integrated intothe parent bacterium. In some alternative embodiments, at least oneduplicated sequence (e.g., a duplicated CRISPR repeat sequence) that isderived, derivable, obtained or obtainable from the parent bacterium'sgenome or one or more of the parent bacterium's plasmids (e.g.,megaplasmids) is also integrated. In some particularly preferredembodiments, at least one duplicated sequence is copied or replicatedfrom the genome of the parent bacterium. In some embodiments, the CRISPRrepeat sequence in a CRISPR locus is duplicated and the tagging sequenceis integrated in the bacterium's genome immediately after (e.g.,downstream) the new duplicated CRISPR repeat. However, it is notintended that the present invention be limited to any specific mechanismor theory of action.

In some highly preferred embodiments, the at least one duplicatedsequence is a CRISPR repeat sequence that has at least about 90%, about95%, about 96%, about 97%, about 98%, or about 99% identity to theCRISPR repeats in the one or more CRISPR loci of the parent bacteriumand/or tagged bacterium. In some particularly preferred embodiments, theat least one duplicated sequence is a CRISPR repeat sequence that has atleast about 100% identity to the CRISPR repeats in the one or moreCRISPR loci of the parent bacterium and/or tagged bacterium. In someembodiments, the duplicated sequence is at least about 24 nucleotides inlength, while in some preferred embodiments, the duplicated sequence isbetween about 24 and about 40 nucleotides in length.

In some preferred embodiments, the at least one tagging sequence and theat least one duplicated sequence are integrated into the parentbacterium. In some embodiments, each time a tagging sequence isintegrated into the genome of the parent bacterium, it is accompanied bythe iterative, sequential, simultaneous or substantially simultaneousintegration of at least one duplicated sequence. Accordingly, at leastone pair of sequences comprising the tagging sequence and the duplicatedsequence is integrated into the parent bacterium, thereby resulting in atagged bacterium. However, it is not intended that the present inventionbe limited to any specific mechanism or means of action.

In some preferred embodiments, the at least one tagging sequence and theat least one duplicated sequence integrate adjacent to each other. Insome particularly preferred embodiments, the at least one taggingsequence and the at least one duplicated sequence integrate directlyadjacent to each other such that there are no intervening nucleotidesbetween the sequences.

In some embodiments, the duplicated sequence is attached, linked orfused to one end (e.g., the 5′ or the 3′ end) of the tagging sequence.In some preferred embodiments, the duplicated sequence is attached,linked or fused to the 5′ end of the tagging sequence. In someparticularly preferred embodiments, fusion of a duplicated sequence witha tagging sequence forms a CRISPR spacer repeat unit. Accordingly, insome embodiments, following the integration of a CRISPR spacer repeatunit, the duplicated sequence is the first sequence at the 5′ end of theCRISPR locus and the tagging sequence is the second (i.e., the next)sequence in the CRISPR locus, downstream of the duplicated sequence. Inyet further preferred embodiments, the sequences within a CRISPR spacerrepeat unit are directly attached, directly linked or directly fusedsuch that there are no intervening nucleotides between the duplicatedsequence and the tagging sequence.

In some particularly preferred embodiments, a CRISPR spacer repeat unitis integrated into the genome of the parent bacterium to produce atagged bacterium. In some preferred embodiments, the duplicated sequenceis derived, derivable, obtained or obtainable from the parentbacterium's genome. In some additional embodiments, the tagging sequenceis derived, derivable, obtained or obtainable from the genome of thebacteriophage that is used to infect the parent bacterium.

In some further embodiments, multiple CRISPR spacer repeat units areintegrated into the genome of the parent bacterium. In some embodiments,the multiple CRISPR spacer repeat units comprise a first CRISPR spacerrepeat unit comprising a duplicated sequence and a tagging sequence anda second CRISPR spacer repeat unit comprising a second duplicatedsequence and a second tagging sequence. In some preferred embodiments,the second duplicated sequence typically has the same sequence (e.g.,greater than about 95%, about 96,%, about 97%, about 98%, about 99%, orabout 100% identity) as the first duplicated sequence. In someembodiments, the tagging sequence typically has a different sequence(e.g., less than about 40%, about 30%, about 20%, about 10%, about 5%,about 4%, about 3%, about 2%, about 1% or about 0% identity) to thefirst tagging sequence. This is also the case in embodiments containingfurther integrated CRISPR spacer repeat unit sequences.

In some preferred embodiments, the configuration of the multiple CRISPRspacer repeat units is typically:

[duplicated sequence-tagging sequence]_(n)

-   -   wherein n=2, 3, 4, 5, or ≧6.

In some particularly preferred, embodiments, the configuration of themultiple CRISPR spacer repeat units is typically:

[CRISPR repeat-tagging sequence]_(n)

-   -   wherein n=2, 3, 4, 5, or ≧6.

In some preferred embodiments, the configuration of the multiple CRISPRspacer repeat units is:

5′-[duplicated sequence-tagging sequence]_(n)-3′

-   -   wherein n=2, 3, 4, 5,or ≧6.

In some particularly preferred embodiments, the configuration of themultiple CRISPR spacer repeat units is:

5′-[CRISPR repeat-tagging sequence]_(n)-3′

-   -   wherein n=2, 3, 4, 5, or ≧6.

In some preferred embodiments, multiple CRISPR spacer repeat units areintegrated into the parent bacterium.

In some embodiments, the tagging sequence portion of the CRISPR spacerrepeat unit is integrated adjacent to: (i) a duplicated sequence that ishomologous (e.g., identical) to a naturally occurring sequence in theparent bacterium; (ii) a duplicated sequence that is homologous (e.g.,identical) to a naturally occurring sequence in the CRISPR locus of theparent bacterium; or (iii) most preferably, a duplicated sequence thatis homologous (e.g., identical) to a naturally occurring CRISPR repeatin the CRISPR locus of the parent bacterium.

Following each exposure of a parent bacterium to a given bacteriophagein independent experiments, the tagging sequence in each of the taggedbacterium is presented a different nucleotide sequence, thereby creatinga sequence that was unique to each bacterium. Thus, upon exposure of aparent bacterium to a given bacteriophage, the tagging sequence that isintegrated into a parent bacterium is selected from the genome of thebacteriophage. As indicated above, it is not intended that the presentinvention be limited to random integration events nor any particularmechanism nor means of action.

This surprising finding was used in the development of the presentinvention, as the selected tagging sequence provides a unique tag orlabel in the tagged bacterium. Surprisingly, it was also found that whenthe same parent bacterium is exposed to the same bacteriophage, thetagging sequence that is integrated in independent/distinct experimentsis of a different sequence, thereby resulting in a unique label in thetagged bacterium following each exposure.

In some embodiments, a randomly selected tagging sequence is identifiedin the tagged bacterium by virtue of one or more of the followingproperties of the tagging sequence: (1) the location of the taggingsequence in the one or more CRISPR loci of the bacteriophage insensitivemutant (as indicated herein, the tagging sequence is typically locatedat one and/or both the 5′ and/or 3′ ends (more preferably, the 5′ end)of the CRISPR locus of the tagged bacterium; (2) the tagging sequencehas a high degree of homology or identity (e.g., 100% identity) to asequence in the bacteriophage genome that the parent bacterium wasexposed to; and/or (3) the tagging sequence is fused, linked or attachedto (e.g., directly fused, linked or attached to) at least one sequence(e.g., a CRISPR repeat; i.e., a “CRISPR spacer repeat unit) that isduplicated from the genome of the parent bacterium. Typically, asdescribed herein, this CRISPR spacer repeat unit is located at oneand/or both ends (e.g., the 5′ and/or 3′ end; more preferably, the 5′end) of the CRISPR locus of the tagged bacterium. Thus, in someembodiments, CRISPR spacer repeat units integrates at both ends of theCRISPR locus of the parent bacterium such that the sequences are at the5′ end and the 3′ end of the CRISPR locus. In some additionalembodiments, one of the duplicated sequences is the first sequence atthe 5′ end of the CRISPR locus and the tagging sequence is locatedimmediately downstream of the duplicated sequence. In some embodiments,the other duplicated sequence is the last sequence at the 3′ end of theCRISPR locus and the tagging sequence is immediately upstream of theduplicated sequence.

In some preferred embodiments, the tagging sequence(s) and/or theduplicated sequence(s) of the CRISPR spacer repeat unit integrate at oneend of the CRISPR locus of the parent bacterium such that thesequence(s) are at the 3′ end of the CRISPR locus. In some furtherembodiments, the duplicated sequence is the last sequence at the 3′ endof the CRISPR locus and the tagging sequence is located immediatelyupstream of the duplicated sequence. In some preferred embodiments, thetagging sequence(s) and/or the duplicated sequence(s) integrate at oneend of the CRISPR locus of the parent bacterium such that the sequencesare at the 5′ end of the CRISPR locus. In some embodiments, theduplicated sequence is the first sequence at the 5′ end of the CRISPRlocus and the tagging sequence is immediately downstream of theduplicated sequence.

As described herein, the tagging sequence(s) is a strain specific tag inthe sense that the tagging sequence that is integrated or inserted fromthe bacteriophage into the parent bacterium is different each time theparent bacterium (e.g., the same parent bacterium) is exposed to thebacteriophage (e.g., the same bacteriophage). Hence, the taggingsequence finds use as a unique tag for a given bacterial strain.

In some embodiments, the tagging sequence(s) and/or the duplicatedsequence(s) integrate into one or more CRISPR loci. In some alternativeembodiments, the tagging sequence(s) and/or the duplicated sequence(s)integrate into one or more different CRISPR loci. In furtherembodiments, two or more different tagging sequence(s) and/or duplicatedsequence(s) integrate into one CRISPR locus. In yet additionalembodiments, two or more different tagging sequence(s) and/or duplicatedsequence(s) each integrate into two or more different CRISPR loci.

L. Tagged CRISPR Loci

The genome of Streptococcus thermophilus LMG18311 contains 3 CRISPRloci; the 36-bp repeated sequences are different in CRISPR1 (34repeats), CRISPR2 (5 repeats), and CRISPR3 (a single sequence).Nevertheless, they are perfectly conserved within each locus. CRISPR1and CRISPR2 repeats are respectively interspaced by 33 and 4 sequencesof 30 bp in length. All these interspacing sequences are different fromeach other. They are also different from those found in strain CNRZ1066(41 interspacing sequences within CRISPR1) and in strain LMD-9 (16within CRISPR1 and 8 within CRISPR3), which both are S. thermophilus.

Streptococcus thermophilus strain DGCC7710 (deposited at the French“Collection Nationale de Cultures de Microorganismes” under number CNCM1-2423) possesses at least 3 CRISPR loci: CRISPR1, CRISPR2, and CRISPR3.In strains CNRZ1066 and LMG18311 for which the complete genome sequenceis known (Bolotin et al., [2004) supra), CRISPR1 is located at the samechromosomal locus: between str0660 (or stu0660) and str0661 (orstu0661). In strain DGCC7710, CRISPR1 is located between highly similargenes. CRISPR1 of strain DGCC7710 contains 33 repeats (including theterminal repeat), and thus 32 spacers. Each of these spacers aredifferent from each other. While most of these spacers are new (i.e.,not previously identified within CRISPR loci), four spacers close to theCRISPR1 trailer are identical to already known CRISPR1 spacers. Thesefour include: the 28^(th) spacer of DGCC7710, which is 100% identical tothe 31^(st) CRISPR1 spacer of strain CNRZ1575 (Genbank accession numberDQ072991); the 30^(th) spacer of DGCC7710, which is 100% identical tothe 27^(th) CRISPR1 spacer of strain CNRZ703 (Genbank accession numberDQ072990); the 31^(st) spacer of DGCC7710, which is 100% identical tothe 28^(th) CRISPR1 spacer of strain CNRZ703 (Genbank accession numberDQ072990); and the 32^(nd) spacer of DGCC7710, which is 100% identicalto the 30^(th) CRISPR1 spacer of strain CNRZ703 (Genbank accessionnumber DQ072990). The CRISPR1 sequence (5′-3′) of strain DGCC7710 isshown in SEQ ID NO:1.

Streptococcus thermophilus strain DGCC7778 was isolated as a naturalphage resistant mutant using DGCC7710 as the parental strain, and phageD858 as the virulent phage. The CRISPR1 of strain DGCC7778 contains 35repeats (including the terminal repeat), and thus 34 spacers. Whencompared to the CRISPR1 sequence of DGCC7710, the CRISPR1 sequence ofDGCC7778 possesses two additional, adjacent, new spacers, as well as twoadditional repeats which flank the new spacers, at one end of the CRISPRlocus (i.e., close to the leader). All of the other spacers of CRISPR1locus are unchanged. The CRISPR1 sequence (5′-3′) of strain DGCC7778 isshown in SEQ ID NO:2.

Thus, in the case of DGCC7778, the first spacer(5′-caacacattcaacagattaatgaagaatac-3′ [SEQ ID NO:3] and the secondspacer (5′-tccactcacgtacaaatagtgagtgtactc-3′ [SEQ ID NO:4]) constitutethe strain-specific tag which identifies this tagged strain. During thedevelopment of the present invention, it was shown that the sequence ofboth new spacers exists within the D858 phage genome. The sequence ofthe second new spacer is located between positions 25471 and 25442 bp(i.e., on the minus strand) of the D858 genome, with one mismatch (96.7%of identical nucleotides over 30 nucleotides). The sequence of the firstspacer is located between positions 31481 and 31410 bp (i.e., on theplus strand) of the D858 genome (100% of identical nucleotides over 30nucleotides). Although it is not intended that the present invention belimited to any particular mechanism nor theory, the fact that two newspacers present in the CRISPR1 locus of DGCC7778 are needed to confer tostrain DGCC7778 resistance to phage D858, it is contemplated that spacer“2” was first inserted into the CRISPR1 locus of DGCC7710 (33 repeatsand 32 spacers), at one end of this CRISPR locus, together with onerepeat. This insertion gave rise to a bacteriophage insensitive mutant(intermediate strain), tagged with this additional new spacer (i.e., nowbearing 34 repeats and 33 spacers). This spacer is derived from the D858genome, but a replication error or reverse transcription error, likelyoccurred during the insertion process, leading to one point mutation.Due to the imperfect match (i.e., 1 mismatch) between this newlyacquired spacer and the targeted phage sequence, the efficiency ofresistance of this intermediate strain to phage D858 was low.

However, a second event of spacer insertion occurred in thisintermediate strain (i.e., the strain more resistant to phage D858 thanparental strain DGCC7710, but not “fully” resistant because of themismatch), leading to the insertion of a second new spacer (the spacer“1” as found in DGCC7778) at the same end of CRISPR1 locus, togetherwith one repeat. This second insertion gave rise to a new bacteriophageinsensitive mutant, which was isolated and named DGCC7778. DGCC7778 ismore resistant to D858 than the intermediate strain, and much moreresistant than parental strain DGCC7710, due to the presence of spacer“1,” which is 100% identical to the targeted phage sequence.

Streptococcus thermophilus strain DGCC7710-RH1 was isolated as a naturalphage resistant mutant using DGCC7710 as the parent strain and phageD858 as the virulent phage. The CRISPR1 of strain DGCC7710-RH1 contains34 repeats (including the terminal repeat), and 33 spacers. Whencompared to the CRISPR1 sequence of Streptococcus thermophilus strainDGCC7710, the CRISPR1 sequence of Streptococcus thermophilus strainDGCC7710-RH1 possesses one additional new spacer (i.e., taggingsequence) and one additional repeat which flanks the new spacer, at oneend of the CRISPR locus (i.e., close to the leader, at the 5′ end of theCRISPR locus). All the other spacers of CRISPR1 locus were unchanged.The CRISPR1 sequence (5′-3′) of strain DGCC7710-RH1 is:

(SEQ ID NO: 5)caaggacagttattgattttataatcactatgtgggtataaaaacgtcaaaatttcatttgagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtcaacaattgcaacatcttataacccacttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtgtttgacagcaaatcaagattcgaattgtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatgacgaggagctattggcacaacttacaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgatttgacaatctgctgaccactgttatcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacacttggcaggcttattactcaacagcgaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACctgttccttgttcttttgttgtatcttttcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACttcattcttccgtttttgtttgcgaatcctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgctggcgaggaaacgaacaaggcctcaacaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcatagagtggaaaactagaaacagattcaaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataatgccgttgaattacacggcaaggtcaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgagcgagctcgaaataatcttaattacaagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgttcgctagcgtcatgtggtaacgtatttaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACggcgtcccaatcctgattaatacttactcgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaacacagcaagacaagaggatgatgctatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgacacaagaacgtatgcaagagttcaagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacaattcttcatccggtaactgctcaagtgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaattaagggcatagaaagggagacaacatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgatatttaaaatcattttcataacttcatGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgcagtatcagcaagcaagctgttagttactGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataaactatgaaattttataatttttaagaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaataatttatggtatagcttaatatcattgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtgcatcgagcacgttcgagtttaccgtttcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtctatatcgaggtcaactaacaattatgctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatcgttcaaattctgttttaggtacatttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatcaatacgacaagagttaaaatggtcttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgcttagctgtccaatccacgaacgtggatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcaaccaacggtaacagctactttttacagtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataactgaaggataggagcttgtaaagtctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtaatgctacatctcaaaggatgatcccagaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaagtagttgatgacctctacaatggtttatGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacctagaagcatttgagcgtatattgattgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaattttgccccttctttgccccttgactagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaccattagcaatcatttgtgcccattgagtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAGTttgattcaacataaaaagccagttcaattgaacttggcttt

The leader sequence of this CRISPR1 is:

5′ caaggacagttattgatmataatcactatgtgggtataaaaacgtcaaaaMcatttgag 3′ (SEQID NO:6). The integrated sequence comprising CRISPR repeats is shown inupper case, while the CRISPR spacers are shown in lower case. In thissequence, the terminal repeat has the sequence 5′gtttttgtactctcaagatttaagtaactgtacagt 3′ (SEQ ID NO:7), while the trailersequence is has the sequence: 5′ttgattcaacataaaaagccagttcaattgaacttggcttt 3′ (SEQ ID NO:8). Thus, for S.thermophilus strain DGCC7710-RH1, the spacer(5′-tcaacaattgcaacatcttataacccactt-3′ [SEQ ID NO:9]) constitutes thestrain-specific tagging sequence which identifies this mutant strain(i.e., the tagged bacterium). The sequence of the new spacer (i.e., thetagging sequence) is present within the D858 phage genome.

The sequence of the spacer is found between positions 31921 and 31950 bp(i.e., on the plus strand) of the D858 genome (and has 100% identity tothe D858 genomic sequence over 30 nucleotides). The new spacer (i.e.,the tagging sequence) that is integrated into the CRISPR1 locus of S.thermophilus strain DGCC7710-RH1 confers resistance to phage D858 tothis strain.

S. thermophilus strain DGCC7710-RH2 was isolated as a natural phageresistant mutant using S. thermophilus strain DGCC7710 as the parentalstrain, and phage D858 as the virulent phage. The CRISPR1 of S.thermophilus strain DGCC7710-RH2 contains 34 repeats (including theterminal repeat) and 33 spacers. When compared to the CRISPR1 sequenceof S. thermophilus strain DGCC7710, the CRISPR1 sequence of S.thermophilus strain DGCC7710-RH2 possesses one additional new spacer(i.e., tagging sequence) and one additional repeat which flanks the newspacer at one end of the CRISPR locus (i.e., close to the leader, at the5′ end of the CRISPR locus). All of the other spacers of CRISPR1 locusare unchanged. The CRISPR1 sequence (5′-3′) of strain DGCC7710-RH2 is:

(SEQ ID NO: 10)caaggacagttattgattttataatcactatgtgggtataaaaacgtcaaaatttcatttgagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACttacgtttgaaaagaatatcaaatcaatgaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtgtttgacagcaaatcaagattcgaattgtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatgacgaggagctattggcacaacttacaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgatttgacaatctgctgaccactgttatcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacacttggcaggcttattactcaacagcgaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACctgttccttgttcttttgttgtatcttttcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACttcattcttccgtttttgtttgcgaatcctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgctggcgaggaaacgaacaaggcctcaacaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcatagagtggaaaactagaaacagattcaaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataatgccgttgaattacacggcaaggtcaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgagcgagctcgaaataatcttaattacaagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgttcgctagcgtcatgtggtaacgtatttaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACggcgtcccaatcctgattaatacttactcgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaacacagcaagacaagaggatgatgctatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgacacaagaacgtatgcaagagttcaagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacaattcttcatccggtaactgctcaagtgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaattaagggcatagaaagggagacaacatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgatatttaaaatcattttcataacttcatGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgcagtatcagcaagcaagctgttagttactGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataaactatgaaattttataatttttaagaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaataatttatggtatagcttaatatcattgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtgcatcgagcacgttcgagtttaccgtttcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtctatatcgaggtcaactaacaattatgctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatcgttcaaattctgttttaggtacatttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatcaatacgacaagagttaaaatggtcttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgcttagctgtccaatccacgaacgtggatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcaaccaacggtaacagctactttttacagtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataactgaaggataggagcttgtaaagtctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtaatgctacatctcaaaggatgatcccagaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaagtagttgatgacctctacaatggtttatGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacctagaagcatttgagcgtatattgattgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaattttgccccttctttgccccttgactagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaccattagcaatcatttgtgcccattgagtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAGTttgattcaacataaaaagccagttcaattgaacttggcttt

The leader sequence is5′caaggacagttattgatittataatcactatgtgggtataaaaacgtcaaaatttcatttgag3′ (SEQID NO:6). The integrated sequences comprising CRISPR repeats are shownin upper case, while the CRISPR spacer (i.e., tagging sequence) is shownin lower case. The terminal repeat has the sequence 5′gttmgtactctcaagamaagtaactgtacagt 3′ (SEQ ID NO:7), and the trailersequence has the sequence 5′ ttgattcaacataaaaagccagttcaattgaacttggcttt3′ (SEQ ID NO:8). Thus, in the case of S. thermophiles strainDGCC7710-RH2, the spacer (5′-ttacgtttgaaaagaatatcaaatcaatga-3′ [SEQ IDNO:11]) constitutes the strain-specific tag which identifies this mutantstrain (i.e., tagged bacterium). It was also shown that the sequence ofthe new spacer exists within D858 phage genome. The sequence of thespacer is located between positions 17215 and 17244 bp (i.e., on theplus strand) of the D858 genome (and has 100% identity to the D858genomic sequence over 30 nucleotides). The new spacer that is integratedinto the CRISPR1 locus of S. thermophiles strain DGCC7710-RH2 confers toresistance to phage D858 to the strain.

In addition to the naturally developed tagged CRISPR loci describedabove, in some embodiments tagged bacteria are produced usingrecombinant DNA techniques as known in the art. For example, in someembodiments, synthetic oligonucleotides are produced and inserted into aculture of parent bacteria to produce tagged bacteria. It is also notintended that the present invention be limited to tagged CRISPR loci, asadditional loci find use in tagging embodiments.

M. Typing

The present invention also provides methods and compositions foridentifying (e.g., typing) a tagged bacterium. In some embodiments,identification involves amplification (e.g., using PCR) the CRISPR locusor a portion thereof. In some embodiments, a first primer is designed tohybridize to a sequence that is located upstream of the first CRISPRrepeat of a CRISPR locus. For example, in some embodiments, the firstprimer hybridizes to part of the common leader sequence of the CRISPRlocus. In alternative embodiments, the first primer hybridizes to aneighboring gene that is located upstream of the CRISPR locus. In someembodiments, a second primer hybridizes downstream from the first CRISPRspacer or the first CRISPR spacer core. In some embodiments, the secondprimer hybridizes in the trailer or even in a downstream neighboringgene. In some preferred embodiments, the second primer hybridizes withinthe CRISPR locus. In some alternative preferred embodiments, the secondprimer at least partially hybridizes to a downstream CRISPR spacer orCRISPR spacer core.

In some particularly preferred embodiments, following amplification, thetagging sequence is identified using any suitable method(s) known in theart. For example, in some embodiments, the tagging sequence isidentified by determining the amplification product restriction pattern.Accordingly in some embodiments, once the DNA comprising the CRISPRlocus or a portion thereof has been amplified, it is digested with oneor more restriction enzymes.

In some additional preferred embodiments, the tagging sequences areidentified using sequencing methods as known in the art. In stillfurther embodiments, hybridization methods well known in the art finduse in the present invention. In some embodiments, methods thatencompass hybridization techniques known in the art for the detectionand/or differentiation of bacterial strains find use, including but notlimited to Southern blotting, shift mobility assays, sequencing assaysusing oligonucleotide arrays, spoligotyping, fluorescent in situhybridization (FISH), heteroduplex tracking assays, and heteroduplexmobility analysis.

In some further preferred embodiments, the identified tagging sequenceis compared with a sequences in at least one phage sequence databaseand/or at least one bacterial sequence database. In some embodiments,the tagging sequence matches with one or more sequences in the phagesequence database but not with sequences in the bacterial sequencedatabase. It is contemplated that as new tagged bacteria are preparedusing the methods provided herein, additional database(s) of labels willfind use in the present invention.

N. Tagged Bacteria

As used herein, the terms “tagged bacteria,” “tagged bacterium,”“labelled bacteria” and “labelled bacterium” are all usedinterchangeably in reference to a parent bacterium or parent bacteria,in which one or more CRISPR loci or a portion thereof have been modified(e.g., mutated) in such a way that it is insensitive to the one or morebacteriophage to which it was exposed.

As described in further detail herein, in some embodiments, the taggedbacterium is exposed to more than one bacteriophage (e.g., eitheriteratively, sequentially or simultaneously), such that it accumulatesone or more genomic modifications within one or more CRISPR loci in sucha way that it becomes insensitive to each of the bacteriophages to whichit has been exposed

To infect cells, a bacteriophage injects or transfers its nucleic acidinto the cell with the phage nucleic acid existing independently of thecell's genome. In some embodiments, infection results in the expression(i.e., transcription and translation) of the bacteriophage nucleic acidwithin the cell and continuation of the bacteriophage life cycle.

In some embodiments of the present invention, following exposure to thebacteriophage, the tagged bacterium has a reduced or no susceptibilityto bacteriophage infection and/or multiplication when compared to theparent bacterium. As used herein, the term “reduced susceptibility tobacteriophage infection and/or multiplication” means that the level ofbacteriophage infection and/or multiplication in the tagged bacteriumdoes not cause a deleterious effect to the tagged bacterium.

Thus, in some embodiments of the present invention, a parent bacteriumis not killed following exposure to the bacteriophage, due to mutationof the parent bacterium in such a way that it becomes insensitive to thebacteriophage.

In some embodiments, the tagged bacterium is insensitive orsubstantially insensitive to further infection and/or multiplication bythe bacteriophage. In additional embodiments, the tagged bacterium isinsensitive or substantially insensitive to one or more of themechanisms that the bacteriophage uses to infect and/or multiply in abacterium. In still further embodiments, the tagged bacterium isinsensitive or substantially insensitive to all of the mechanisms thatthe bacteriophage uses to infect and/or multiply in a bacterium. In yetadditional embodiments, the tagged bacterium develops one or moremechanisms that attenuate, inactivate or destroy the bacteriophageduring the infection cycle. In some further embodiments, the presentinvention provides tagged strains selected by standard screeningprocedures that are known in the art to isolate bacteriophageinsensitive mutants.

As indicated above, in addition to the naturally developed tagged CRISPRloci described above, in some embodiments tagged bacteria are producedusing recombinant DNA techniques as known in the art. For example, insome embodiments, synthetic oligonucleotides are produced and insertedinto a culture of parent bacteria to produce tagged bacteria. It is alsonot intended that the present invention be limited to tagged CRISPRloci, as additional loci find use in tagging embodiments.

O. Cultures

Cultures, in particular starter cultures, are used extensively in thefood industry in the manufacture of fermented products including milkproducts (e.g., yogurt and cheese), meat products, bakery products,wine, and vegetable products. In particular, starter cultures findwidespread use in the manufacture of many fermented milk, cheese andbutter products. These bacterial starter cultures impart specificfeatures to various dairy products by performing a number of functions.In some particularly preferred embodiments, the cultures used in thepresent invention are “industrially useful” cultures. As used herein,this term refers to any bacterial culture that finds use in anyindustry, including but not limited to the production of food, feed,cosmetics, pharmaceuticals, neutraceuticals, probiotics, enzymes,metabolites, etc. Indeed, it is not intended that the present inventionbe limited to any particular culture or industry, as the presentinvention finds use in numerous applications.

Commercial non-concentrated cultures of bacteria are referred to inindustry as “mother cultures,” and are propagated at the production site(e.g., a dairy), before being added to an edible starting material(e.g., milk), for fermentation. The starter culture propagated at theproduction site for inoculation into an edible starting material isreferred to as the “bulk starter.”

Suitable starter cultures for use in the present invention include anyorganism which is suitable for use in the food, cosmetic and/orpharmaceutical industry. In some preferred embodiments, the starterculture finds use in the dairy industry. Indeed, cultures of lactic acidbacteria are commonly used in the manufacture of fermented milk products(e.g., buttermilk, yogurt and sour cream), and in the manufacture ofbutter and cheese (e.g., brie, havarti, cheddar, Monterey jack, etc.).

As used herein the term “lactic acid bacteria” refers to Gram positive,microaerophillic or anaerobic bacteria which ferment sugar with theproduction of acids, including lactic acid as the predominantly producedacid, acetic acid, formic acid and propionic acid. The industrially mostuseful lactic acid bacteria include Lactococcus (e.g., Lactococcuslactis), Lactobacillus, Bifidobacterium, Streptococcus, Leuconostoc,Pediococcus, and Propionibacterium species. In some embodiments, thepresent invention provides starter cultures comprising at least onelactic acid bacteria species such as, L. lactis, Lactobacillusdelbrueckii subsp. bulgaricus and Streptococcus thermophilus orcombinations thereof. Lactic acid bacteria starter cultures are commonlyused in the food industry as mixed strain cultures comprising one ormore species. In some embodiments comprising mixed strain cultures(e.g., yogurt starter cultures) comprising strains of Lactobacillusdelbrueckii subsp. bulgaricus and Streptococcus thermophilus, asymbiotic relationship exists between the species wherein the productionof lactic acid is greater compared to cultures of single strain lacticacid bacteria (See e.g., Rajagopal et al., J. Dairy Sci., 73:894-899[1990]).

In some particularly preferred embodiments, the starter culture is alactic acid bacteria species, including but not limited to strains ofBifidobacterium, Brevibacterium, or Propionibacterium. Suitable startercultures of the lactic acid bacteria group include, but are not limitedto commonly used strains Lactococcus, Streptococcus, Lactobacillus(e.g., Lactobacillus acidophilus), Enterococcus, Pediococcus,Leuconostoc, and Oenococcus. Lactococcus species include, but are notlimited to the widely used Lactococcus lactis, including Lactococcuslactis subsp. lactis and Lactococcus lactis subsp. cremoris,andLactococcus lactis subsp. lactis biovar. Other lactic acid bacteriaspecies include Leuconostoc, Streptococcus thermophilus, Lactobacillusdelbrueckii subsp. bulgaricus and Lactobacillus helveticus. In addition,probiotic strains such as Bifidobacterium lactis, Lactobacillusacidophilus, Lactobacillus casei find use in flavor enhancement andprovide health benefits. Thermophilic cultures of lactic acid bacteriacommonly used in the manufacture of Italian cheeses such as Pasta filataor parmesan, include S. thermophilus and L. delbrueckii subspbulgaricus. In some embodiments, other Lactobacillus species (e.g., L.helveticus) are added during manufacturing to obtain a desired flavor.

In some embodiments, the starter culture comprises or consists of agenetically modified strain (prepared according to the methods desiredherein) of one of the above lactic acid bacteria strains or any othersuitable starter culture strain. As known to those skilled in the art,the selection of organisms for the starter cultures used in the presentinvention depends on the particular type of products to be prepared andtreated. Thus, for example, for cheese and butter manufacturing,mesophillic cultures of Lactococcus species, Leuconostoc species andLactobacillus species find wide use, whereas thermophillic strains ofStreptococcus species and of Lactobacillus species find wide use foryogurt and other fermented milk products.

In some embodiments, the starter culture is a dried starter, while inother embodiments, it is a concentrated starter, and in otherembodiments, it is a frozen culture. In some preferred embodiments, thedried starter cultures comprise at least one lactic acid bacteria. Insome embodiments, the starter culture is used for direct inoculation. Insome preferred embodiments, the culture is a concentrated starterculture used for direct inoculation.

In some embodiments, the bacterial starter culture comprises onebacterial strain or species (i.e., it is a pure culture). Thus, in theseembodiments, substantially all, or at least a significant portion of thebacterial starter culture comprises the same bacterial strain orspecies. However, in some alternative embodiments, the starter culturecomprises more than one or several bacterial strains or species (i.e.,it is a mixed culture, such as a defined mixed

Starter cultures prepared using any suitable technique known in the artfind use in the present invention (See e.g., U.S. Pat. No. 4,621,058).For example, starter cultures prepared by the introduction of aninoculum (e.g., a bacterial culture) to a growth medium, to produce aninoculated medium and incubating the inoculated medium to produce astarter culture. However, it is not intended that the present inventionbe limited to any particular method for preparing starter cultures.

Dried starter cultures prepared using any suitable technique known inthe art find use in the present invention (See e.g., U.S. Pat. Nos.4,423,079 and 4,140,800). In some embodiments, the dried startercultures used in the present invention are solid preparations (e.g.,tablets, pellets, capsules, dusts, granules and powders, any of whichare wettable, spray-dried, freeze-dried or lyophilized in someembodiments). In some alternative embodiments, the dried startercultures of the present invention are either a deep frozen pellet orfreeze-dried powder. These dried starter cultures are prepared using anysuitable method known in the art.

In some embodiments, the starter cultures used in the present inventioncomprise concentrates having substantially high concentrations of atleast one bacterial species. In some preferred embodiments, theconcentrates are diluted with water or resuspended in water or anothersuitable diluent (e.g., an appropriate growth medium, mineral oil, orvegetable oil), for use in the present invention. In some embodiments,the concentrated dried starter cultures of the present invention areprepared using methods well known in the art, including, but not limitedto centrifugation, filtration or a combination of such techniques.

P. Products

The present invention finds use in the production of various products,including but not limited to food, feed, cosmetic products, and/orpharmaceutical products. Indeed, it is contemplated that any productprepared from or comprises a bacterial culture finds use in the presentinvention. These include, but are not limited to, fruits, legumes,fodder crops and vegetables including derived products, grain andgrain-derived products, dairy foods and dairy-derived products, meat,poultry, seafood, cosmetics, enzymes, metabolites, and pharmaceuticalproducts.

As used herein, the term “food” is used in a broad sense and includesfeed, foodstuffs, food ingredients, food supplements, and functionalfoods. Although the term includes food for humans, it is intended thatthe term also encompass food for non-human animals (i.e., “feed”).However, in some preferred embodiments, the present invention providesfood for human consumption. As used herein, the term “food ingredient”includes a formulation suitable for addition to foods. In someembodiments, the formulations are used at low levels in a wide varietyof products that require, for example, acidifying or emulsifying. Asused herein, the term “functional food” refers to foods that are capableof providing not only a nutritional effect and/or a taste satisfaction,but are also capable of delivering a further beneficial effect toconsumer. In some embodiments the bacteria of the present inventioncomprise or are added to a food ingredient, supplement or functionalfood. It is contemplated that the food be provided in any suitable form,including but not limited to solutions, solids, gels, emulsions, etc.,depending on the use and/or the mode of application and/or the mode ofadministration. Indeed, it is not intended that the present invention belimited to food in any particular form. In some embodiments, thebacteria of the present invention find use in the numerous preparationof food products, including but not limited to confectionery products,dairy products, meat products, poultry products, fish products, andbakery products. In some embodiments, the bacteria are used asingredients in soft drinks, fruit juices, beverages comprising wheyprotein, health teas, cocoa drinks, milk drinks, lactic acid bacteriadrinks, cheese, yogurt, drinking yogurt and wine. In some furtherembodiments, the present invention provides methods of preparing food,including methods that comprise admixing bacteria according to thepresent invention with a food ingredient (e.g., a starting material fora food). In some preferred embodiments, the food provided herein is adairy product. In some particularly preferred embodiments, the dairyproduct is selected from yogurt, cheese (e.g., an acid curd cheese, ahard cheese, a semi-hard cheese, a cottage cheese), a buttermilk, quark,a sour cream, kefir, a fermented whey-based beverage, a koumiss, a milkdrink and a yogurt drink.

As used herein, the terms “food” and “feed” include, but are not limitedto raw and processed plant material, as well as non-plant material. Itis intended that the food/feed be suitable for consumption by anyanimal, human or non-human. In some preferred embodiments, the food/feedfind use with livestock (e.g., cattle, sheep, pigs, etc.), poultry(e.g., chickens and turkeys), fish, reptiles, or crustaceans. Indeed, itis not intended that the present invention be limited to food/feed forany particular organism.

EXPERIMENTAL

The following examples are provided in order to demonstrate and furtherillustrate certain preferred embodiments and aspects of the presentinvention and are not to be construed as limiting the scope thereof.

In the experimental disclosure which follows, the followingabbreviations apply: ° C. (degrees Centigrade); H₂O (water); aa (aminoacid); bp (base pair); kb (kilobase pair); kD (kilodaltons); g and gm(grams); μg and ug (micrograms); mg (milligrams); ng (nanograms); μl andul (microliters); ml (milliliters); mm (millimeters); nm (nanometers);μm and um (micrometer); M (molar); mM (millimolar); μM and uM(micromolar); sec and s (seconds); min(s) (minute/minutes); hr(s)(hour/hours); MOI (multiplicity of infection); EOP (efficiency ofplaquing); PFU (plaque-forming units); MgCl₂ (magnesium chloride); NaCl(sodium chloride); PAGE (polyacrylamide gel electrophoresis); PBS(phosphate buffered saline [150 mM NaCl, 10 mM sodium phosphate buffer,pH 7.2]); SDS (sodium dodecyl sulfate); Tris(tris(hydroxymethyl)aminomethane); w/v (weight to volume); v/v (volumeto volume); Promega (Promega, Inc., Madison, Wis.); ATCC (American TypeCulture Collection, Manassas, Va.); Difco (Difco Laboratories, Detroit,Mich.); GIBCO BRL or Gibco BRL (Life Technologies, Inc., Gaithersburg,Md.); and Sigma (Sigma Chemical Co., St. Louis, Mo.).

The present invention utilizes, unless otherwise indicated, conventionaltechniques of chemistry, molecular biology, microbiology, recombinantDNA and immunology, which are within the capabilities of a person ofordinary skill in the art. Such techniques are well known to those ofskill in the art.

As used herein, DGCC7710 is also referred to as “WT”; DGCC7710RH1 isalso referred to as “DGCC7710-RH1” and “RH1”; DGCC7710RH2 is alsoreferred to as “DGCC7710-RH2” and “RH-2.”

Example 1 Tagging of Streptococcus thermophilus DGCC7710 UsingBacteriophage D2972 by the Insertion of a Single Repeat-Spacer UnitWithin CRISPR1

In this example, S. thermophilus strain DGCC7710 (deposited at theFrench “Collection Nationale de Cultures de Microorganismes” numberedCNCM 1-2423) was tagged by “natural” insertion within its CRISPR1 locusof an additional repeat-spacer unit with the spacer originating frombacteriophage D2972. The DGCC7710 CRISPR1 locus contains 33 repeats(including the terminal repeat) and 32 spacers (See, GenBank AccessionNumber: EF434469). Bacteriophage D2972 was isolated from a fermenteddairy product using strain DGCC7710. Its genome has been fully sequenced(See, GenBank Accession Number: AY699705). The sequence of the DGCC7710CRISPR1 locus is:

(SEQ ID NO: 1)caaggacagttattgattttataatcactatgtgggtataaaaacgtcaaaatttcatttgagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtgtttgacagcaaatcaagattcgaattgtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatgacgaggagctattggcacaacttacaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgatttgacaatctgctgaccactgttatcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacacttggcaggcttattactcaacagcgaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACctgttccttgttcttttgttgtatcttttcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACttcattcttccgtttttgtttgcgaatcctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgctggcgaggaaacgaacaaggcctcaacaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcatagagtggaaaactagaaacagattcaaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataatgccgttgaattacacggcaaggtcaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgagcgagctcgaaataatcttaattacaagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgttcgctagcgtcatgtggtaacgtatttaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACggcgtcccaatcctgattaatacttactcgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaacacagcaagacaagaggatgatgctatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgacacaagaacgtatgcaagagttcaagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacaattcttcatccggtaactgctcaagtgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaattaagggcatagaaagggagacaacatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcgatatttaaaatcattttcataacttcatGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgcagtatcagcaagcaagctgttagttactGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataaactatgaaattttataatttttaagaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaataatttatggtatagcttaatatcattgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtgcatcgagcacgttcgagtttaccgtttcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtctatatcgaggtcaactaacaattatgctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatcgttcaaattctgttttaggtacatttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaatcaatacgacaagagttaaaatggtcttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgcttagctgtccaatccacgaacgtggatgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcaaccaacggtaacagctactttttacagtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACataactgaaggataggagcttgtaaagtctGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtaatgctacatctcaaaggatgatcccagaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaagtagttgatgacctctacaatggtttatGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacctagaagcatttgagcgtatattgattgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaattttgccccttctttgccccttgactagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaccattagcaatcatttgtgcccattgagtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAGTttgattcaacataaaaagccagttcaattgaacttggcttt

In the first step the parental strain (DGCC7710) was exposed to thedonor bacteriophage (D2972). DGCC7710 was pre-cultivated in sterilemilk-based medium (10% w/v of milk powder in water, sterilized for 20min at 110° C.) at 42° C. for 6 hours. The pre-culture was used toinoculate 10 ml of sterile milk-based medium at about 0.05% (w/v). About10⁷ bacteriophages D2972 were added to the inoculated milk-based medium(final bacteriophage count of about 10⁶ pfu/ml). The mixture was thencultivated at 42° C. for 16 hours. Following incubation, dilutions ofthe culture are plated on M17-glucose (0.5% w/v) medium in order toobtain isolated colonies after incubation at 42° C. for 24 hours. Anumber of colonies were picked and grown separately in sterilemilk-based medium at 42° C. for 18 hours to provide a stock of isolates.

Then, each tagged strain was identified through sequence analysis oftheir CRISPR1 loci. In this Example, a tagged strain is a variant of theparental strain, in which the variant contains an additionalrepeat-spacer unit within the CRISPR1 locus (See, FIG. 3). Typically,the spacer part of the additional unit is of approximately 30nucleotides in size and its sequence is identical to a subsequence ofthe donor phage. Isolates were cultivated separately at 42° C. for 18hours in M17-glucose medium. Cells were harvested and their DNAextracted. For each isolate, the region of the chromosome correspondingto the leader end of the CRISPR1 locus was amplified by PCR using thefollowing primers: forward primer yc70 (5′-tgctgagacaacctagtctctc-3′[SEQ ID NO:15]; See, Bolotin et al., Microbiol., 151:2551-2561 [2005]);and reverse primer CR1-89R5 (5′-acaaaaacggaagaatgaagttg-3′ [SEQ IDNO:16]). The PCR reaction mix (final volume of 25 μL) contained: Mg-freebuffer 1× (Promega), MgCl₂ 2.5 mM, each of the four dNTP 2 mM, DNA 10 to100 ng, each primer 0.2 μM, Taq polymerase 1.25 U (Promega). PCR cyclingconditions were as following: pre-denaturation at 98° C. for 5 min, then33 cycles alternating denaturation at 94° C. for 30 s, hybridization at56° C. for 30 s, and elongation at 72° C. for 1 min; followed by a finalelongation step at 72° C. for 4 min. The nucleic sequence of each PCRfragment was then determined using the “forward primer” and classicalsequencing methodology, as known in the art. Each sequence was comparedto that obtained for the parental strain to identify the presence ofadditional sequence.

Through independent experiments, multiple tagged strains were createdfrom DGGC7710 using D2972 as a donor. Some of these tagged strains aredescribed in Table 1-1. They all differ from the parental strain by asingle additional repeat-spacer unit at the leader end of the CRISPR1locus. In all cases, the spacer part of the additional unit is 100%identical to a sub-sequence of the donor bacteriophage D2972 (thissub-sequence of the donor bacteriophage is also referred to as a“pro-spacer”). Typically, the tagged strains described in this Examplepossess a CRISPR1 locus made of 34 repeats and 33 spacers; 32 spacersoriginate from the DGCC7710, the supplementary spacer originates fromD2972.

TABLE 1-1 Description of Strains Tagged in CRISPR1 Locus Derived FromDGCC7710 Using D2972 as a Donor Tagged Parental Donor Inserted donor DNAStrain Strain Phage Sequence Location* DGCC7710_(phi2972) ^(+S40)DGCC7710 D2972 TCTGGAAAGCATATTGAGGGA 27974-28003 (+) GCTACTCTT (SEQ IDNO: 17) DGCC7710_(phi2972) ^(+S41) DGCC7710 D2972 TCTAATCCCACTAGGAATAGT25693-25722 (+) GGGTAGTAA (SEQ ID NO: 18) DGCC7710_(phi2972) ^(+S43)DGCC7710 D2972 TTATAACATAACGGTTAGTTG 23410-23382 (−) GCCTCTAT (SEQ IDNO: 19) DGCC7710_(phi2972) ^(+S44) DGCC7710 D2972 AAGGAGCTAGCCACATTTCCG23334-23363 (+) CAATTGATA (SEQ ID NO: 20) DGCC7710_(phi2972) ^(+S45)DGCC7710 D2972 CAGCTTGAAATGTTTATTGAA 24624-24653 (+) GCAGCAGTG (SEQ IDNO: 21) DGCC7710_(phi2972) ^(+S46) DGCC7710 D2972 AAATCAGTTTTTTGTTCAGAA25582-25611 (+) ACTTGTTCT (SEQ ID NO: 22) *(+/−): indicates the strandof the phage chromosome

Example 2 Tagging of Streptococcus thermophilus DGCC7710 UsingBacteriophage D858 by the Insertion of a Single Repeat-Spacer UnitWithin CRISPR1

In this Example, S. thermophilus strain DGCC7710 was tagged by “natural”insertion within its CRISPR1 locus with an additional repeat-spacer unitwherein the spacer originated from bacteriophage D858. BacteriophageD858 is was isolated from a fermented dairy product in strain DGCC7710.D858 is a bacteriophage belonging to the Siphoviridae family of viruses.Its genome sequence has been completely determined (GenBank Accession.Number: EF529515). This phage is virulent to S. thermophilus strainDGCC7710.

Its genome has been fully sequenced

First, the parental strain (DGCC7710) was exposed to the donorbacteriophage (D858). DGCC7710 was pre-cultivated in sterile milk-basedmedium (10% w/v of milk powder in water, sterilized 20 min at 110° C.)at 42° C. for 6 hours. The pre-culture was used to inoculate 10 ml ofsterile milk-based medium at about 0.05% (w/v). About 10⁷ D858bacteriophages were added to the inoculated milk-based medium (finalbacteriophage count of about 10⁶ pfu/ml). The mixture was thencultivated at 42° C. for 16 hours. Following incubation, dilutions ofthe culture were plated on M17-glucose (0.5% w/v) medium in order toobtain isolated colonies after incubation at 42° C. for 24 hours. Anumber of colonies were picked and grown separately in sterilemilk-based medium at 42° C. for 18 hours to provide a stock of isolates.

Then, each tagged strain was identified through sequence analysis oftheir CRISPR1 locus. In this Example, a tagged strain is a variant ofthe parental strain that contains an additional repeat-spacer unitwithin its CRISPR1 locus (See, FIG. 3). Typically, the spacer part ofthe additional unit was approximately 30 nucleotides in size and itssequence was identical to a sub-sequence of the donor phage. Isolateswere cultivated separately at 42° C. for 18 hours in M 17-glucosemedium. Cells were harvested and their DNA extracted. For each isolate,the region of the chromosome corresponding to the leader end of theCRISPR1 locus was amplified by PCR using the following primers: forwardprimer yc70 (5′-tgctgagacaacctagtctctc-3′ [SEQ ID NO:15], Bolotin etal., [2005], supra); and reverse primer CR1-89R5(5′-acaaaaacggaagaatgaagttg-3′ [SEQ ID NO:20]). The PCR reaction mix(final volume of 25 μL) contained: Mg-free buffer 1× (Promega), MgCl₂2.5 mM, each of the four dNTP 2 mM, DNA 10 to 100 ng, each primer 0.2μM, Taq polymerase 1.25 U (Promega). PCR cycling conditions were asfollowing: pre-denaturation at 98° C. for 5 min, then 33 cyclesalternating denaturation at 94° C. for 30 s, hybridisation at 56° C. for30 s, and elongation at 72° C. for 1 min; followed by a final elongationstep at 72° C. for 4 min. The nucleic sequence of each PCR fragment wasthen determined using the “forward primer” and classical sequencingmethodology as known in the art. Each sequence was compared to thatobtained for the parental strain to identify the presence of additionalsequence.

One tagged strain created from DGCC7710 using D858 as a donor isdescribed in Table 2-1. It differs from the parental strain by a singleadditional repeat-spacer unit at the leader end of the CRISPR1 locus.The spacer part of the additional unit is 100% identical to asub-sequence of the donor bacteriophage D858.

TABLE 2-1 Description of Strains Tagged in CRISPR1 Locus, Derived FromDGCC7710 and Using D858 as a Donor Tagged Parental Donor Inserted DonorDNA Strain Strain Phage Sequence Location* DGCC7710_(phi858) ^(+S42)DGCC7710 D858 TCGATAAATCAGCCAAAGTATT 27560-27589 (+) AAGTGGTT (SEQ IDNO: 23) *(+/−): indicates the strand of the phage chromosome

Example 3 Tagging of Streptococcus thermophilus DGCC7710 UsingBacteriophage D2972 by the Insertion of Multiple Repeat-Spacer UnitsWithin CRISPR1

In this Example, S. thermophilus strain DGCC7710 was tagged by “natural”insertion within its CRISPR1 locus by the addition of multiplerepeat-spacer units with the spacers originating from bacteriophageD2972.

First, the parental strain (DGCC7710) was exposed to the donorbacteriophage (D2972). DGCC7710 was pre-cultivated in sterile milk-basedmedium (10% w/v of milk powder in water, sterilized 20 min at 110° C.)at 42° C. for 6 hours. The pre-culture was used to inoculate 10 ml ofsterile milk-based medium at about 0.05% (w/v). About 10⁷ D2972bacteriophages were added to the inoculated milk-based medium (finalbacteriophage count of about 10⁶ pfu/ml). The mixture was thencultivated at 42° C. for 16 hours. Following incubation, dilutions ofthe culture were plated on M17-glucose (0.5% w/v) medium in order toobtain isolated colonies after incubation at 42° C. for 24 hours. Anumber of colonies were picked and grown separately in sterilemilk-based medium at 42° C. for 18 hours to provide a stock of isolates.

Then, each tagged strain was identified through sequence analysis of itsCRISPR1 locus. In this Example, a tagged strain is a variant of theparental strain that contains multiple additional repeat-spacer unitswithin its CRISPR1 locus (See, FIG. 3). Typically, the spacer part ofeach additional unit was approximately 30 nucleotides in size and itssequence was identical to a sub-sequence of the donor phage. Isolateswere cultivated separately at 42° C. for 18 hours in M17-glucose medium.Cells were harvested and their DNA extracted. For each isolate, theregion of the chromosome corresponding to the leader end of the CRISPR1locus is amplified by PCR using the following primers: forward primeryc70 (5′-tgctgagacaacctagictctc-3′ [SEQ ID NO:15], Bolotin et al., 2005,supra); reverse primer CR1-89R5 (5′-acaaaaacggaagaatgaagttg-3′ [SEQ IDNO:16]). The PCR reaction mix (final volume of 25 μL) contained: Mg-freebuffer 1× (Promega), MgCl₂ 2.5 mM, each of the four dNTP 2 mM, DNA 10 to100 ng, each primer 0.2 μM, Taq polymerase 1.25 U (Promega). PCR cyclingconditions were as following: pre-denaturation at 98° C. for 5 min, then33 cycles alternating denaturation at 94° C. for 30 s, hybridization at56° C. for 30 s, and elongation at 72° C. for 1 min; followed by a finalelongation step at 72° C. for 4 min. The nucleic sequence of each PCRfragment was then determined using the “forward primer” and classicalsequencing methodology as known in the art. Each sequence was comparedto that obtained for the parental strain to identify the presence ofadditional sequence.

Through independent experiments, multiple tagged strains were createdfrom DGCC7710 using D2972 as a donor. Some of these tagged strains aredescribed in Table 3-1. They all differ from the parental strain bymultiple additional repeat-spacer units at the leader end of the CRISPR1locus. In all cases, the spacer part of each additional unit is 100%identical to a subsequence of the donor bacteriophage D2972.

TABLE 3-1 Description of Tagged Strains in CRISPR1 Locus From DGCC7710Using D2972 as a Donor Tagged Parental Donor Inserted Donor DNA StrainStrain Phage Sequence Location DGCC7710_(phi2972) ^(+S46+S47) DGCC7710D2972 AAATCAGTTTTTTGTTCAGAAACTTG 33045-33073 (+) TTCT (SEQ ID NO: 24)25582-25611 (+) TTGTCTATTACGACAACATGGAAGA TGAT (SEQ ID NO: 25)DGCC7710_(phi2972) ^(+S48+S49) DGCC7710 D2972 TTTTGAGAAAGTCTTTAACGATGCA25967-25938 (−) GTAGC (SEQ ID NO: 26) 6008-6037 (+)TAATAGTTTACCAAATCATCTTTATT CCAA (SEQ ID NO: 27) DGCC7710_(phi2972)^(+S50+S51) DGCC7710 D2972 GAAGTTGAAATAATTCGAGAAATAG 34105-34134 (+)AACTC (SEQ ID NO: 28) 29246-29275 (+) TGGAAACCAAGAAATGCAATAGAAT GGAAG(SEQ ID NO: 29) DGCC7710_(phi2972) ^(+S52+S4) DGCC7710 D2972CTGATTGTTAATGTACGAGGGCTCC 31582-31611 (+) AGCCA (SEQ ID NO: 30)21732-21703 (−) CTCAGTCGTTACTGGTGAACCAGTTT CAAT (SEQ ID NO: 31)DGCC7710_(phi2972) ^(+S53+S54) DGCC7710 D2972 TGTTTCAAGGTTTCGGGTCCAAGTAT29647-29618 (−) CATT (SEQ ID NO: 32) 16681-16652 (−)TTTTCCGTCTTCTTTTTTAGCAAAGA TACG (SEQ ID NO: 33) DGCC7710_(phi2972)^(+S61+S62) DGCC7710 D2972 GATTCGTGGCGATATTCGTCTTACGT 31709-31737 (+)TTGA (SEQ ID NO: 34) 17182-17211 (+) ACATATCGACGTATCGTGATTATCCC ATT (SEQID NO: 35) DGCC7710_(phi2972) ^(+S55+S63+S41) DGCC7710 D2972CTGGAAAGCATATTGAGGGAGCTAC 25693-25722 (+) TCTT (SEQ ID NO: 36) 1114-1142(+) GTATATCGAAGAACGACTGAAAGAG 27381-27409 (+) CTTGA (SEQ ID NO: 37)TCTAATCCCACTAGGAATAGTGGGT AGTAA (SEQ ID NO: 38) *(+/−): indicates thestrand of the phage chromosome

Example 4 Tagging of Streptococcus thermophilus DGCC7710 UsingBacteriophage D2972 by the Iterative Insertion of Repeat-Spacer UnitsWithin CRISPR1

In this Example, S. thermophilus strain DGCC7710 was tagged by “natural”means through iterative insertion within its CRISPR1 locus of additionalrepeat-spacer units with the spacers originating from bacteriophageD2972 and from bacteriophages derived from D2972.

In the first iteration, the parental strain (DGCC7710) was exposed tothe donor bacteriophage (D2972) and a tagged strain was isolated andcharacterized by using the same methodology as described in Example 1.Compared to DGCC7710, this tagged strain (named DGCC7710_(phi2972)^(S6)) possessed an additional repeat-spacer unit as described in Table4 in its CRISPR1 locus

Because of the insertion of an additional repeat-spacer unit in theCRISPR1 locus of strain DGCC7710_(phi2972) ^(S6) , the donorbacteriophage D2972 was no longer virulent against DGCC7710_(phi2972)^(S6), and cannot be used as a donor bacteriophage for this strain. Thisproblem was overcome by the use of a mutated donor phage derived fromD2972 that includes at least one specific modification within its genome(i.e., a “mutated phage”). This mutated phage was selected by exposingthe donor bacteriophage to the tagged strain, such that a modification(i.e., mutation) of the parental phage renders it virulent for thetagged strain.

DGCC7710_(phi2972) ^(S6) was pre-cultivated in milk-based medium at 42°C. for 18 hours. A milk-based medium was then inoculated with thepre-culture of DGCC7710_(phi2972) ^(S6) at a concentration of about 10⁶cfu/ml and with a suspension of D2972 at an MOI (multiplicity ofinfection) greater than 100. The culture was incubated at 42° C. for 18hours, and then centrifuged for 10 min at 10,000×g. The supernatant washarvested and filtered using a 0.45 μm filter. Appropriate dilutions ofthe filtrated supernatant were used to inoculate a M17-glucose agarmedia seeded with a lawn of DGCC7710_(phi2972) ^(S6) using methods wellknown in the art. The seeded agar plates were incubated for 24 hours at42° C. One isolated plaque was picked and cultivated onDGCC7710_(phi2972) ^(S6) in M 17- glucose medium for 6 hours at 42° C. Asuspension of this new bacteriophage named D4724 was obtained byfiltering the culture through a 0.45 μm filter. The virulence of D4724against DGCC7710_(phi2972) ^(S6) was verified.

Next, strain DGCC7710_(phi2972) ^(S6) was exposed to the donorbacteriophage D4724 and a tagged strain was isolated and characterizedusing the methodology described in Example 1. Compared to DGCC7710 thistagged strain (named DGCC7710_(phi2972) ^(S6) _(phi4724) ^(S15))possesses in its CRISPR1 locus 2 additional repeat-spacer units asdescribed in Table 4-1.

For the purpose of a third iteration, a second mutated bacteriophagenamed D4733 was selected through challenging of DGCC7710_(phi2972) ^(S6)_(phi4724) ^(S15) by D4724 using the same methodology as for obtainingD4724. Bacteriophage D4733 is virulent against DGCC7710_(phi2972) ^(S6)_(phi4724) ^(S15). Upon exposure of virulent for DGCC7710_(phi2972)^(S6) _(phi4724) ^(S15) to the donor bacteriophage D4733, a taggedstrain was isolated and characterized using the same methodology asdescribed in Example 1. Compared to DGCC7710, this tagged strain, namedDGCC7710_(phi2972) ^(S6) _(phi4724) ^(S15) _(phi4733) ^(S29), possessed3 additional repeat-spacer units in its CRISPR1 locus as described inTable 4-1.

TABLE 4-1 Description of Iteratively Tagged Strains in CRISPR1 Locusfrom DGCC7710 Using D2972 and Mutated Phages D4724 and D4733 as DonorBacteriophages Tagged Parental Donor Inserted Donor DNA Strain StrainPhage Sequence Location DGCC7710_(phi2972) ^(+S6) DGCC7710 D2972GCCCTTCTAATTGGA 34521-34492 TTACCTTCCGAGGTG (−) (SEQ ID NO: 39)DGCC7710_(phi2972) ^(+S56) _(phi4724) ^(+S20) DGCC7710_(phi2972) ^(+S6)D4724 GCCCTTCTAATTGGA 34521-34492 TTACCTTCCGAGGTG (−) (SEQ ID NO: 40)1113-1142 TTATATCGAAGAACG (+) ACTGAAAGAGCTTGA (SEQ ID NO: 41)DGCC7710_(phi2972) ^(+S6) _(phi4724) ^(+S20) _(phi4733) ^(+S29)DGCC7710_(phi2972) ^(+S6) _(phi4724) ^(+S20) D4733 GCCCTTCTAATTGGA34521-34492 TTACCTTCCGAGGTG (−) (SEQ ID NO: 42) 1113-1142TTATATCGAAGAACG (+) ACTGAAAGAGCTTGA 32136-32164 (SEQ ID NO: 43) (+)ATTGGCATGATTTCAA TTTTAATTGGGAT (SEQ ID NO: 44) *(+/−): indicates thestrand of the phage chromosome

Example 5 Tagging of Streptococcus thermophilus DGCC3198 UsingBacteriophage D4241 by the Insertion of a Single Repeat-Spacer Unitwithin CRISPR1

In this Example, S. thermophilus strain DGCC3198 (also known as LMD-9and deposited at the American Type Culture Collection as ATCC BAA-365)was tagged by “natural” insertion within its CRISPR1 locus of anadditional repeat-spacer unit with the spacer originating frombacteriophage D4241. The DGCC3198 CRISPR1 locus contains 17 repeats(including the terminal repeat) and 16 spacers (GenBank AccessionNumber: CP000419). Bacteriophage D4241 was isolated from a fermenteddairy product using strain DGCC3198. The sequence of the DGCC3198CRISPR1 locus is:

(SEQ ID NO: 45)caagaacagttattgattttataatcactatgtgggtatgaaaatctcaaaaatcatttgagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACatgatgatgaagtatcgtcatctactaacGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACcttcacctcaaatcttagagctggactaaaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACatgtctgaaaaataaccgaccatcattactGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACgaagctcatcatgttaaggctaaaacctatGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtagtctaaatagatttcttgcaccattgtaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACattcgtgaaaaaatatcgtgaaataggcaaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtctaggctcatctaaagataaatcagtagcGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtaaaaacatggggcggcggtaatagtgtaagGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACacaaccagcaaagagagcgccgacaacattGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACtataacacaggtttagaggatgttatacttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACctagaagctcaagcggtaaaagttgatggcgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACctttgagggcaagccctcgccgttccatttGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaactaccaagcaaatcagcaatcaataagtGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACctataagtgacaatcagcgtagggaatacgGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACatcagtgcggtatatttaccctagacgctaGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAACaacagttactattaatcacgattccaacggGTTTTTGTACTCTCAAGATTTAAGTAACTGTACAGTttgattcaacataaaaagccggttcaattgaacttggcttt

The parental strain (DGCC3198) was exposed to the donor bacteriophage(D4241) as described in Example 1. Using the methods described inExample 1, isolates were obtained and further analyzed. PCR reactionsand DNA sequence determination were performed as described in Example 1,except that the reverse primer used for the PCR was CR122-R3, with thefollowing sequence: 5′-gctctaagatttgaggtgaagg-3′ (SEQ ID NO:46).

Multiple tagged strains were created from DGCC3198 using D4241 as adonor. These tagged strains are described in Table 5-1. All of thesetagged strains differ from the parental strain by a single additionalrepeat-spacer unit at the leader end of the CRISPR1 locus. For the 3 newspacer sequences described in Table 5-1, a homology search withsequences available from public database displayed the best homologyscores with sub-sequences of the S. thermophilus bacteriophage DTI(GenBank Accession Number AF085222), confirming that the new spacersequence originated from the bacteriophage.

TABLE 5-1 Description of Tagged Strains in CRISPR1 Locus from DGCC3198Using D4241 as Donor Bacteriophages Tagged Parental Donor Strain StrainPhage Inserted Donor DNA Sequence DGCC3198_(phi4241) ^(+S64) DGCC3198D4241 ACCAAGTAGCATTTGAGCAAAGATAGATTG (SEQ ID NO: 47) DGCC3198_(phi4241)^(+S65) DGCC3198 D4241 TAGATCTCATGAGTGGCGACAGTGAGCTT (SEQ ID NO: 48)DGCC3198_(phi4241) ^(+S66) DGCC3198 D4241 TACCATCTTGGGATAGGTACTGGTCATGCC(SEQ ID NO: 49)

Example 6 Tagging of Streptococcus thermophilus DGCC3198 UsingBacteriophage D4241 by the Insertion of a Single Repeat-Spacer UnitWithin CRISPR3

In this Example, S. thermophilus strain DGCC3198 was tagged by “natural”insertion within its CRISPR3 locus of an additional repeat-spacer unitwith the spacer originating from bacteriophage D4241. DGCC3198 CRISPR3locus contains 9 repeats (including the terminal repeat) and 8 spacers(GenBank Accession Number: CP000419). The sequence of the DGCC3198CRISPR3 locus is:

(SEQ ID NO: 50)taaattggtaataagtatagatagtcttgagttatttcaagactatcttttagtatttagtagtttctgtatgaagttgaatgggataatcattttgttagagagtagattataaggatttgatagaggaggaattaagttgcttgacatatgattattaagaaataatctaatatggtgacagtcacatcttgtctaaaacgttgatatataaggatttttaaggtataataaatataaaaatggaattattttgaagctgaagtcatgctgagattaatagtgcgattacgaaatctggtagaaaagatatcctacgagGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACggtgaaaaaggttcactgtacgagtacttaGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACtcaatgagtggtatccaagacgaaaacttaGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACccttgtcgtggctctccatacgcccatataGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACtgtttgggaaaccgcagtagccatgattaaGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACacagagtacaatattgtcctcattggagacacGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACctcatattcgttagttgcttttgtcataaaGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACagaactttatcaagataaaactactttaaaGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACatagtattaatttcattgaaaaataattgtGTTTTAGAGCTGTGTTGTTTCGAATGGTTCCAAAACttttgttatcacaattttcggttgacatctcttagaactcatcttatcataaaggagtctagtattgaaatgtgagaagggac

The parental strain (DGCC3198) was exposed to the donor bacteriophage(D4241) as described in Example 1. Using the methods described inExample 1, isolates were obtained and further analyzed. PCR reactionsand DNA sequence determination were performed as described in Example 1,except that CR3lead-F1 (5′-ctgagattaatagtgcgattacg-3′; SEQ ID NO:51) andCR3trail-R2 (5′-gctggatattcgtataacatgtc-3′; SEQ ID NO:52) were used.

One tagged strain was created from DGCC3198 using D4241 as a donor. Thistagged strain is described in Table 6-1. This tagged strain differs fromthe parental strain by a single additional repeat-spacer unit at theleader end of the CRISPR3 locus. For the new spacer sequence describedin Table 6, a homology search with sequences available from publicdatabase displayed the best homology scores with sub-sequences of the S.thermophiles bacteriophage DT1 and Sfi19 (GenBank Accession NumberAF085222 and AF115102), confirming that the new spacer sequenceoriginated from the bacteriophage.

TABLE 6-1 Description of Tagged Strain in CRISPR3 Locus From DGCC3198Using D4241 as Donor Bacteriophages Tagged Parental Strain Strain DonorPhage Inserted Donor DNA Sequence DGCC3198_(phi4241) ^(+S67) DGCC3198D4241 5′-tgcaatttccattagttcttgacgcccttt-3′ (SEQ ID NO: 53)

Example 7 PCR Method for Specific Detection of Tagged Strains

In this Example, PCR methods for specific detection of tagged strainsare described. When a strain is naturally tagged by the addition of oneor more unique oligonucleotide sequence(s) made of the added spacers inone or more of the CRISPR1 loci, it is necessary to be able to detectthe tagged strains. The methods are based on the presence of sequencesspecific to the tagged strains that are inserted within a preciselyidentified region of the chromosome of the strain. Therefore, a specificPCR amplification method is designed that is specific to the taggedstrain. A strain devoid of this unique oligonucleotide sequence resultsin no PCR amplified DNA, whereas PCR using the tagged strain DNA resultsin the amplification of a DNA fragment of a defined length.

To set up the specific PCR detection method, 2 primers are designed. Oneof the primers is the forward primer and is unspecific to the taggedstrain but specific to a CRISPR locus; it is designated “CRISPR primer.”In S. thermophilus, and depending on the tagged strain, the “CRISPRprimer” is identical to a sequence within the CRISPR1 locus (“CRISPR1primer”) or within the CRISPR3 locus (“CRISPR3 primer”) or within theCRISPR2 locus (“CRISPR2 primer”). The CRISPR primers are chosen amongsequences that are conserved among strains of the species of interest.For S. thermophilus, the following primers are recommended: CRISPR1primer, 5′-tgctgagacaacctagtctctc-3′ (yc70, Bolotin et al., [2005],supra [SEQ ID NO:15]); CRISPR3 primer,5′-ctgagattaatagtgcgattacg-3′(CR3lead-F1; SEQ ID NO:51). The secondprimer is the reverse primer and is specific to the tagged strain; it isdesignated “TAG primer”. The TAG primers are complementary to one of thespacers of the added repeat-spacer units in the tagged strains.Preferably, the TAG primer is complementary to the spacer of the addedrepeat-spacer unit that is the more distal from the leader sequence ofthe CRISPR locus. FIG. 4 illustrates the location of the CRISPR primerand the TAG primer.

Table 7-1 provides examples of TAG primers for the detection of taggedstrains listed in Example 1 to 6.

TABLE 7-1 Primers Used for the Detection of Tagged Strains Described inExample 1 to 6. Tagged Strain CRISPR Primer TAG PrimerDGCC7710_(phi2972) ^(+S40) 5′-tgctgagacaacctagtctctc-3′5′-aagagtagctccctcaatatgc-3′ (SEQ ID NO: 15) (SEQ ID NO: 54)DGCC7710_(phi2972) ^(+S41) 5′-tgctgagacaacctagtctctc-3′5′-ttactacccactattcctagtg-3′ (SEQ ID NO: 15) (SEQ ID NO: 55)DGCC7710_(phi2972) ^(+S43) 5′-tgctgagacaacctagtctctc-3′5′-atagaggccaactaaccgttat-3′ (SEQ ID NO: 15) (SEQ ID NO: 56)DGCC7710_(phi2972) ^(+S44) 5′-tgctgagacaacctagtctctc-3′5′-tatcaattgcggaaatgtggct-3′ (SEQ ID NO: 15) (SEQ ID NO: 57)DGCC7710_(phi2972) ^(+S45) 5′-tgctgagacaacctagtctctc-3′5′-cactgctgcttcaataaacatt-3′ (SEQ ID NO: 15) (SEQ ID NO: 58)DGCC7710_(phi2972) ^(+S46) 5′-tgctgagacaacctagtctctc-3′5′-agaacaagtttctgaacaaaaa-3′ (SEQ ID NO: 15) (SEQ ID NO: 59)DGCC7710_(phi858) ^(+S42) 5′-tgctgagacaacctagtctctc-3′5′-aaccacttaatactttggctga-3′ (SEQ ID NO: 15) (SEQ ID NO: 60)DGCC7710_(phi2972) ^(+S46+S47) 5′-tgctgagacaacctagtctctc-3′5′-agaacaagtttctgaacaaaaa-3′ (SEQ ID NO: 15) (SEQ ID NO: 61)DGCC7710_(phi2972) ^(+S48+S49) 5′-tgctgagacaacctagtctctc-3′5′-gctactgcatcgttaaagactt-3′ (SEQ ID NO: 15) (SEQ ID NO: 62)DGCC7710_(phi2972) ^(+S50+S51) 5′-tgctgagacaacctagtctctc-3′5′-gagttctatttctcgaattatt-3′ (SEQ ID NO: 15) (SEQ ID NO: 63)DGCC7710_(phi2972) ^(+S52+S4) 5′-tgctgagacaacctagtctctc-3′5′-tggctggagccctcgtacatta-3′ (SEQ ID NO: 15) (SEQ ID NO: 64)DGCC7710_(phi2972) ^(+S53+S54) 5′-tgctgagacaacctagtctctc-3′5′-aatgatacttggacccgaaacc-3′ (SEQ ID NO: 15) (SEQ ID NO: 65)DGCC7710_(phi2972) ^(+S61+S62) 5′-tgctgagacaacctagtctctc-3′5′-tcaaacgtaagacgaatatcgc-3′ (SEQ ID NO: 15) (SEQ ID NO: 66)DGCC7710_(phi2972) ^(+S55+S63+S41) 5′-tgctgagacaacctagtctctc-3′5′-aagagtagctccctcaatatgc-3′ (SEQ ID NO: 15) (SEQ ID NO: 54)DGCC7710_(phi2972) ^(+S6) 5′-tgctgagacaacctagtctctc-3′5′cacctcggaacctaatccaatt-3′ (SEQ ID NO: 15) (SEQ ID NO: 67)DGCC7710_(phi2972) ^(+S6) _(phi4724) ^(+S20)5′-tgctgagacaacctagtctctc-3′ 5′-cacctcggaacctaatccaatt-3′ (SEQ ID NO:15) (SEQ ID NO: 67) DGCC7710_(phi2972) ^(+S6) _(phi4724) ^(+S20)_(phi4733) ^(+S29) 5′-tgctgagacaacctagtctctc-3′5′-cacctcggaacctaatccaatt-3′ (SEQ ID NO: 15) (SEQ ID NO: 67)DGCC3198_(phi4241) ^(+S64) 5′-tgctgagacaacctagtctctc-3′5′-caatctatctttgctcaaatgc-3′ (SEQ ID NO: 15) (SEQ ID NO: 67)DGCC3198_(phi4241) ^(+S65) 5′-tgctgagacaacctagtctctc-3′5′-aagctcactgtcgccactctag-3′ (SEQ ID NO: 15) (SEQ ID NO: 68)DGCC3198_(phi4241) ^(+S66) 5′-tgctgagacaacctagtctctc-3′5′-ggcatgccagtacctatcccaa-3′ (SEQ ID NO: 15) (SEQ ID NO: 69)DGCC3198_(phi4241) ^(+S67) 5′-ctgagattaatagtgcgattacg-3′ (SEQ5′-tcaagaactaatggaaattgcag-3′ ID NO: 51) (SEQ ID NO: 70)

In these experiments, the sample containing the strain to be detectedwas treated using any suitable method known in the art in order to sortthe bacteria from the rest of the sample. As an example in case ofyogurt or fresh dairy samples containing S. thermophilus, the sample wastreated as described by Lick et al., (Lick et al., Milchwissenschaft50:183-186 [1996]).

Depending on the amount of bacteria contained within the resultingmaterial, S. thermophilus cells were amplified through cultivation inM17-glucose medium for 18 hours at 42° C. The DNA was then extractedfrom the bacteria and submitted to the specific PCR. The PCR primers(CRISPR primer and TAG primer) were chosen appropriately as described inTable 7-1. The PCR reaction mix (final volume of 25 μL) contained:Mg-free buffer 1× (Promega), MgCl₂ 2.5 mM, each of the four dNTP 2 mM,DNA 10 to 100 ng, each primer 0.2 μM, Taq polymerase 1.25 U (Promega).PCR cycling conditions were: pre-denaturation at 98° C. for 5 min,followed by 33 cycles alternating denaturation at 94° C. for 30 s,hybridization at 56° C. for 30 s, and elongation at 72° C. for 1 min;followed by a final elongation step at 72° C. for 4 min. In a controlPCR, the extracted DNA was submitted to second PCR targeting 16S RNAgenes using the following universal primers: BSF8-20,5′-agagtttgatcctggctcag-3′ (SEQ ID NO:71) and BSR1541-20,5′-aaggaggtgatccagccgca-3′ (SEQ ID NO:72; See, Wilmotte et al., FEBSLett., 317:96-100 [1993]).

The PCR reaction mix (final volume of 25 μL) contained: Mg-free buffer1× (Promega), MgCl₂ 2.5 mM, each of the four dNTP 2 mM, DNA 10 to 100ng, each primer 0.2 μM, Taq polymerase 1.25 U (Promega). PCR cyclingconditions were as follows: pre-denaturation at 95° C. during 7 min,followed by 35 cycles of alternating denaturation at 95° C. during 1min, hybridisation at 58° C. during 1 min 30s, and elongation at 72° C.for 2 mM 30 s; followed by a final elongation step at 72° C. for 5 min.The PCR amplification products were then analyzed using agarose (1%,w/v) gel electrophoresis and the size of the amplified DNA fragments wasrecorded. For each specific PCR, controls were made using DNA extractedfrom the parental strain (DGCC7710 or DGCC3198 depending on the taggedstrain) and from one of the tagged strain (DGCC_(phi2972) ^(S6)).

The results are presented in Table 7-2. Each of the PCR reactions wasspecific to the tested tagged strain, since PCR products of appropriatesize were always obtained in control PCRs and specific PCRs onlyresulted in amplified DNA fragment when specific tagged strain DNA wasused.

TABLE 7-2 Size of the PCR Products Obtained Through Specific PCR andControl PCR on Tagged Strain DNA, Parental Strain DNA and DGCC_(phi2972)^(S6) DNA Specific Tagged DGCC_(phi2972) ^(S6) Parental Strain DNA DNAStrain DNA Specific Control Specific Control Specific Control SpecificPCR^(c) PCR^(a) PCR^(a) PCR^(a) PCR^(a) PCR^(a) PCR^(a)DGCC7710_(phi2972) ^(+S40) 240 1530 0 1530  0^(b) 1530DGCC7710_(phi2972) ^(+S41) 240 1530 0 1530 0 1530 DGCC7710_(phi2972)^(+S43) 240 1530 0 1530 0 1530 DGCC7710_(phi2972) ^(+S44) 240 1530 01530 0 1530 DGCC7710_(phi2972) ^(+S45) 240 1530 0 1530 0 1530DGCC7710_(phi2972) ^(+S46) 240 1530 0 1530 0 1530 DGCC7710_(phi858)^(+S42) 240 1530 0 1530 0 1530 DGCC7710_(phi2972) ^(+S46+S47) 310 1530 01530 0 1530 DGCC7710_(phi2972) ^(+S48+S49) 310 1530 0 1530 0 1530DGCC7710_(phi2972) ^(+S50+S51) 310 1530 0 1530 0 1530 DGCC7710_(phi2972)^(+S52+S4) 310 1530 0 1530 0 1530 DGCC7710_(phi2972) ^(+S53+S54) 3101530 0 1530 0 1530 DGCC7710_(phi2972) ^(+S61+S62) 310 1530 0 1530 0 1530DGCC7710_(phi2972) ^(+S55+S63+S41) 370 1530 0 1530 0 1530DGCC7710_(phi2972) ^(+S6) 240 1530 240 1530 0 1530 DGCC7710_(phi2972)^(+S6) _(phi4724) ^(+S20) 310 1530 0 1530 0 1530 DGCC7710_(phi2972)^(+S6) _(phi4724) ^(+S20) _(phi4733) ^(+S29) 370 1530 0 1530 0 1530DGCC3198_(phi4241) ^(+S64) 240 1530 0 1530 0 1530 DGCC3198_(phi4241)^(+S65) 240 1530 0 1530 0 1530 DGCC3198_(phi4241) ^(+S66) 240 1530 01530 0 1530 DGCC3198_(phi4241) ^(+S67) 105 1530 0 1530 0 1530^(a)approximate size of the amplified fragment in base pairs; ^(b)0means no PCR fragment detected; ^(c)using the specific PCR primer asmentioned in Table 7-1.

Example 8 Method for the Identification of Tagged Strains

In this Example, a method is described for detecting the presence oftagged strains in a sample and to identify their nature. This is donethrough the PCR amplification of one or more of CRISPR loci and thepartial sequence determination. This method finds use in variousembodiments, as while the method described in Example 7 is useful forthe detection of a tagged strain, it may not be sufficient for itsformal identification. In addition in some cases, the nature of thetagged strain contained within the sample is not known. Thus, thespecific PCR method cannot be used for its detection. Eventually, thetagged strain can be detected and identified through the analysis of themodified CRISPR locus.

S. thermophilus cells contained within a sample were extracted from thesample using suitable method known in the art and were plated atappropriate dilutions on agar M17-glucose agar then were incubated for24 hours at 42° C. in order to obtained isolated colonies. One or moreisolated colonies were then picked and grown in liquid M17-glucosemedium for 18 hours at 42° C. From each culture, cells were harvestedand their DNA extracted. For each isolate, the region of the chromosomecorresponding to the CRISPR1 locus was amplified by PCR using thefollowing primers: forward primer yc70 (5′-tgctgagacaacctagtctctc-3′[SEQ ID NO:15], Bolotin et al., [2005]; supra); and reverse primerSPIDR-dws (5′-taaacagagcctccctatcc-3′ [SEQ ID NO:73]). The PCR reactionmix (final volume of 25 μL) contained: Mg-free buffer 1× (Promega),MgCl₂ 2.5 mM, each of the four dNTP 2 mM, DNA 10 to 100 ng, each primer0.2 μM, Tag polymerase 1.25 U (Promega). PCR cycling conditions were asfollows: pre-denaturation at 98° C. for 5 min, followed by 33 cyclesalternating denaturation at 94° C. for 30 s, hybridization at 56° C. for30 s, and elongation at 72° C. for 1 min; followed by a final elongationstep at 72° C. for 4 min. In some cases, the region corresponding to theCRISPR3 locus was amplified using the following primers: CR3lead-F1,5′-ctgagattaatagtgcgattacg-3′ (SEQ ID NO:51) and CR3trail-R2,5′-gctggatattcgtataacatgtc-3′ (SEQ ID NO:52). The nucleic acid sequenceof each PCR fragment was then determined using the “forward primer” andclassical sequencing methodology, as known in the art. Each sequence wasthen compared to sequences of CRISPR loci available in databases.

In one experiment, the CRISPR1 locus from an isolate obtained from afermented milk product was submitted to PCR and the resulting ampliconwas submitted to sequencing. The sequence was compared to that ofsequences available in databases. FIG. 5 provides the results of thecomparison. It appeared that the sequence was 100% identical to that ofstrain DGCC7710, with one additional sequence of 66 nucleotides. This 66nucleotide sequence is made of 36 nucleotides in its 5′end that areidentical to that of the repeats in the S. thermophilus CRISPR1 locusand the 30 remaining nucleotide sequence is identical to a sub-sequenceof the bacteriophage D2972. Moreover, this 66 nucleotide-additionalsequence was located immediately downstream of the leader sequence ofCRISPR1. Consequently, the CRISPR1 locus of the isolate contains theCRISPR1 locus of DGCC7710 with one additional repeat-spacer unit asdescribed in FIG. 3. In addition, the 30 remaining nucleotide sequencewas also identical to the additional spacer sequence of the taggedstrain DGCC_(phi2972) ^(S41). This conclusively indicated that theisolate obtained from the fermented milk product was the tagged strainDGCC_(phi2972) ^(S41).

All patents and publications mentioned in the specification areindicative of the levels of those skilled in the art to which theinvention pertains. All patents and publications are herein incorporatedby reference to the same extent as if each individual publication wasspecifically and individually indicated to be incorporated by reference.

Those of skill in the art readily appreciate that the present inventionis well adapted to carry out the objects and obtain the ends andadvantages mentioned, as well as those inherent therein. Thecompositions and methods described herein are representative ofpreferred embodiments, are exemplary, and are not intended aslimitations on the scope of the invention. It is readily apparent to oneskilled in the art that varying substitutions and modifications may bemade to the invention disclosed herein without departing from the scopeand spirit of the invention.

The invention illustratively described herein suitably may be practicedin the absence of any element or elements, limitation or limitationswhich is not specifically disclosed herein. The terms and expressionswhich have been employed are used as terms of description and not oflimitation, and there is no intention that in the use of such terms andexpressions of excluding any equivalents of the features shown anddescribed or portions thereof, but it is recognized that variousmodifications are possible within the scope of the invention. Thus, itshould be understood that although the present invention has beenspecifically disclosed by preferred embodiments and optional features,modification and variation of the concepts herein disclosed may beresorted to by those skilled in the art, and that such modifications andvariations are considered to be within the scope of this invention.

The invention has been described broadly and generically herein. Each ofthe narrower species and subgeneric groupings falling within the genericdisclosure also form part of the invention. This includes the genericdescription of the invention with a proviso or negative limitationremoving any subject matter from the genus, regardless of whether or notthe excised material is specifically recited herein.

We claim:
 1. A labelled bacterium comprising two or more additional repeat-spacer units integrated into a clustered regularly spaced short palindromic repeat (CRISPR) locus, as compared to the CRISPR locus of a parent bacterium from which the labelled bacterium is derived, wherein said spacer is a label, wherein said labelled bacterium is obtained or obtainable by a method comprising the steps of: (a) exposing the parent bacterium to a bacteriophage the parent bacterium is sensitive to; (b) selecting a bacteriophage insensitive mutant; (c) comparing a CRISPR locus or a portion thereof from the parent bacterium and the bacteriophage insensitive mutant; and (d) selecting a labelled bacterium comprising an additional repeat-spacer unit in the CRISPR locus that is not present in the CRISPR locus of the parent bacterium; wherein said method comprises exposing the parent bacterium to two or more bacteriophages the parent bacteria is sensitive to, either simultaneously or sequentially and wherein a labelled bacterium comprising two or more additional repeat-spacer units is selected; and wherein the labelled bacterium is insensitive to said two or more bacteriophages.
 2. A cell culture comprising a labelled bacterium according to claim
 1. 3. The cell culture according to claim 2, wherein said cell culture is a starter culture, a probiotic culture or a dietary supplement.
 4. A food product or feed comprising the labelled bacterium according to claim
 1. 5. A process for preparing a food product or feed comprising the step of adding the labelled bacterium according to claim 1 or the cell culture according to claim 2 or claim 3 to said food product or feed.
 6. The labelled bacterium according to claim 1, wherein the parent bacterium is selected from the group of genera consisting of: Escherichia, Shigella, Salmonella, Erwinia, Yersinia, Bacillus, Vibrio, Legionella, Pseudomonas, Neisseria, Bordetella, Helicobacter, Listeria, Agrobacterium, Staphylococcus, Streptococcus, Enterococcus, Clostridium, Corynebacterium, Mycobacterium, Treponema, Borrelia, Francisella, Brucella, Bifidobacterium, Brevibacterium, Propionibacterium, Lactococcus, Lactobacillus, Pediococcus, Leuconostoc and Oenococcus.
 7. The labelled bacterium according to claim 1 wherein the parent bacterium is Streptococcus thennophilus.
 8. A dairy product comprising the labelled bacterium according to claim
 1. 9. A starter culture comprising a labelled bacterium comprising two or more additional repeat-spacer units integrated into a clustered regularly spaced short palindromic repeat (CRISPR) locus, as compared to the CRISPR locus of a parent bacterium from which the labelled bacterium is derived, wherein said spacer is a label, wherein said labelled bacterium is obtained or obtainable by a method comprising the steps of: (a) exposing the parent bacterium to a bacteriophage the parent bacterium is sensitive to; (b) selecting a bacteriophage insensitive mutant; (c) comparing a CRISPR locus or a portion thereof from the parent bacterium and the bacteriophage insensitive mutant; and (d) selecting a labelled bacterium comprising an additional repeat-spacer unit in the CRISPR locus that is not present in the CRISPR locus of the parent bacterium; wherein said method comprises exposing the parent bacterium to two or more bacteriophages the parent bacterium is sensitive to, either simultaneously or sequentially and wherein a labelled bacterium comprising two or more additional repeat-spacer units is selected; and wherein the labelled bacterium is insensitive to said two or more bacteriophages.
 10. The starter culture according to claim 9, wherein the starter culture is a defined mixed culture.
 11. A probiotic culture comprising a labelled bacterium comprising two or more additional repeat-spacer units integrated into a clustered regularly spaced short palindromic repeat (CRISPR) locus, as compared to the CRISPR locus of a parent bacterium from which the labelled bacterium is derived, wherein said spacer is a label, wherein said labelled bacterium is obtained or obtainable by a method comprising the steps of: (a) exposing the parent bacterium to a bacteriophage the parent bacterium is sensitive to; (b) selecting a bacteriophage insensitive mutant; (c) comparing a CRISPR locus or a portion thereof from the parent bacterium and the bacteriophage insensitive mutant; and (d) selecting a labelled bacterium comprising an additional repeat-spacer unit in the CRISPR locus that is not present in the CRISPR locus of the parent bacterium; wherein said method comprises exposing the parent bacterium to two or more bacteriophages the parent bacterium is sensitive to, either simultaneously or sequentially and wherein a labelled bacterium comprising two or more additional repeat-spacer units is selected; and wherein the labelled bacterium is insensitive to said two or more bacteriophages.
 12. A dietary supplement culture comprising a labelled bacterium comprising two or more additional repeat-spacer units integrated into a clustered regularly spaced short palindromic repeat (CRISPR) locus, as compared to the CRISPR locus of a parent bacterium from which the labelled bacterium is derived, wherein said spacer is a label, wherein said labelled bacterium is obtained or obtainable by a method comprising the steps of: (a) exposing the parent bacterium to a bacteriophage the parent bacterium is sensitive to; (b) selecting a bacteriophage insensitive mutant; (c) comparing a CRISPR locus or a portion thereof from the parent bacterium and the bacteriophage insensitive mutant; and (d) selecting a labelled bacterium comprising an additional repeat-spacer unit in the CRISPR locus that is not present in the CRISPR locus of the parent bacterium; wherein said method comprises exposing the parent bacterium to two or more bacteriophages the parent bacterium is sensitive to, either simultaneously or sequentially and wherein a labelled bacterium comprising two or more additional repeat-spacer units is selected; and wherein the labelled bacterium is insensitive to said two or more bacteriophage.
 13. A frozen starter culture comprising a labelled bacterium comprising two or more additional repeat-spacer units integrated into a clustered regularly spaced short palindromic repeat (CRISPR) locus, as compared to the CRISPR locus of a parent bacterium from which the labelled bacterium is derived, wherein said spacer is a label, wherein said labelled bacterium is obtained or obtainable by a method comprising the steps of: (a) exposing the parent bacterium to a bacteriophage the parent bacterium is sensitive to; (b) selecting a bacteriophage insensitive mutant; (c) comparing a CRISPR locus or a portion thereof from the parent bacterium and the bacteriophage insensitive mutant; and (d) selecting a labelled bacterium comprising an additional repeat-spacer unit in the CRISPR locus that is not present in the CRISPR locus of the parent bacterium; wherein said method comprises exposing the parent bacterium to two or more bacteriophages the parent bacterium is sensitive to, either simultaneously or sequentially and wherein a labelled bacterium comprising two or more additional repeat-spacer units is selected; and wherein the labelled bacterium is insensitive to said two or more bacteriophages.
 14. A dried starter culture comprising a labelled bacterium comprising two or more additional repeat-spacer units integrated into a clustered regularly spaced short palindromic repeat (CRISPR) locus, as compared to the CRISPR locus of a parent bacterium from which the labelled bacterium is derived, wherein said spacer is a label, wherein said labelled bacterium is obtained or obtainable by a method comprising the steps of: (a) exposing the parent bacterium to a bacteriophage the parent bacterium is sensitive to; (b) selecting a bacteriophage insensitive mutant; (c) comparing a CRISPR locus or a portion thereof from the parent bacterium and the bacteriophage insensitive mutant; and (d) selecting a labelled bacterium comprising an additional repeat-spacer unit in the CRISPR locus that is not present in the CRISPR locus of the parent bacterium; wherein said method comprises exposing the parent bacterium to two or more bacteriophages the parent bacterium is sensitive to, either simultaneously or sequentially and wherein a labelled bacterium comprising two or more additional repeat-spacer units is selected; and wherein the labelled bacterium is insensitive to said two or more bacteriophages.
 15. A freeze dried starter culture comprising a labelled bacterium comprising two or more additional repeat-spacer units integrated into a clustered regularly spaced short palindromic repeat (CRISPR) locus, as compared to the CRISPR locus of a parent bacterium from which the labelled bacterium is derived, wherein said labelled bacterium is obtained or obtainable by a method comprising the steps of: (a) exposing the parent bacterium to a bacteriophage the parent bacterium is sensitive to; (b) selecting a bacteriophage insensitive mutant; (c) comparing a CRISPR locus or a portion thereof from the parent bacterium and the bacteriophage insensitive mutant; and (d) selecting a labelled bacterium comprising an additional repeat-spacer unit in the CRISPR locus that is not present in the CRISPR locus of the parent bacterium; wherein said method comprises exposing the parent bacterium to two or more bacteriophages the parent bacterium is sensitive to either simultaneously or sequentially and wherein a labelled bacterium comprising two or more additional repeat-spacer units is selected; and wherein the labelled bacterium is insensitive to said two or more bacteriophages.
 16. The labelled bacterium according to claim 1, wherein the two or more additional repeat-spacer units are integrated at the 5′ end of the CRISPR locus.
 17. The labelled bacterium according to claim 1, wherein the two or more additional repeat-spacer units are integrated at the 3′ end of the CRISPR locus.
 18. The labelled bacterium according to claim 1, wherein the two or more additional repeat-spacer units are integrated into one CRISPR locus.
 19. The labelled bacterium according to claim 1, wherein the two or more additional repeat-spacer units are integrated into several CRISPR loci. 